SLC2A1 variant information please help!

General
1

SLC2A1:c.1373G>A /rs752143706

SNV:1-42927147-C-T(GRCh38)

This variant was identified in a prenatal case and is classified as pathogenic.

The variant is reported in 8 alleles in gnomAd v.4.1

I am looking for any information critical for risk assessment and counseling of the parents .It is quite urgent because the pregnancy is 33 week already. no abnormal findings on ultrasound.

Specifically, I would greatly appreciate the following information:

  • are the reports derived from a biobank or from a specific cohort of patients?

  • Any evidence of penetrance?

  • was it inherited or de novo?

  • was the quality of the variant calls good enough?

This information is essential for estimating the risk of severe disease in the fetus and for guiding parental decision-making. The pregnancy is already at an advanced gestational age, so time is an important factor.

2

For this particular variant, you can infer that three of the eight alleles were present in samples from the UK Biobank by toggling between the full gnomAD v4.1 dataset and the non-UK Biobank subset of gnomAD v4.1.

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We are unable to share the cohort of origin for the other five alleles (see previous response here).

The quality metrics of this variant call can be found at the bottom of the variant page:

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The variant carriers appear to have high genotype quality and adequate depth for their genotype calls. The allele balance for their calls also falls within the expectations for a true heterozygous call. The available read data also suggest that these are high quality variant calls.