chr3-22847961-T-C

Variant names:

• chr3-22847961-T-C
• rs620918

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 0.484 in 152,010 control chromosomes in the GnomAD database, including 18,368 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 0.48 (18368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73505 AN: 151892 Hom.: 18353 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.484 AC: 73564 AN: 152010 Hom.: 18368 Cov.: 32 AF XY: 0.486 AC XY: 36113 AN XY: 74312

African (AFR) AF: 0.511 AC: 21171 AN: 41460

American (AMR) AF: 0.610 AC: 9305 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3594 AN: 5180

South Asian (SAS) AF: 0.541 AC: 2605 AN: 4818

European-Finnish (FIN) AF: 0.359 AC: 3788 AN: 10542

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29881 AN: 67984

Other (OTH) AF: 0.481 AC: 1013 AN: 2104

Alfa AF: 0.462 Hom.: 46799

Bravo AF: 0.504

Asia WGS AF: 0.624 AC: 2153 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.79
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs620918; hg19: chr3-22889452;