3-102016803-T-C

Variant names:

• chr3-102016803-T-C
• rs771757

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.801 in 152,070 control chromosomes in the GnomAD database, including 49,162 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 0.80 (49162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121684 AN: 151952 Hom.: 49134 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.801 AC: 121765 AN: 152070 Hom.: 49162 Cov.: 31 AF XY: 0.805 AC XY: 59811 AN XY: 74304

African (AFR) AF: 0.688 AC: 28491 AN: 41420

American (AMR) AF: 0.859 AC: 13137 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3101 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5167 AN: 5180

South Asian (SAS) AF: 0.884 AC: 4250 AN: 4810

European-Finnish (FIN) AF: 0.842 AC: 8912 AN: 10580

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55933 AN: 68002

Other (OTH) AF: 0.812 AC: 1716 AN: 2114

Alfa AF: 0.820 Hom.: 124985

Bravo AF: 0.798

Asia WGS AF: 0.933 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs771757; hg19: chr3-101735647;