rs3093726

Positions:

• chr6-31579012-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0283 in 152,310 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.028 (67 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0283 (4314/152310) while in subpopulation SAS AF= 0.0524 (253/4830). AF 95% confidence interval is 0.0471. There are 67 homozygotes in gnomad4. There are 2076 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 67 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4313 AN: 152192 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0154

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.00999

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.00979

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0297

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0283 AC: 4314 AN: 152310 Hom.: 67 Cov.: 32 AF XY: 0.0279 AC XY: 2076 AN XY: 74462

Gnomad4 AFR AF: 0.0189

Gnomad4 AMR AF: 0.0154

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.0524

Gnomad4 FIN AF: 0.00979

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0326 Hom.: 9

Bravo AF: 0.0280

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3093726; hg19: chr6-31546789;