rs6819266

Variant names:

• chr4-62476552-G-C
• rs6819266

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 0.456 in 151,778 control chromosomes in the GnomAD database, including 17,246 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 0.46 (17246 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69105 AN: 151660 Hom.: 17199 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.456 AC: 69207 AN: 151778 Hom.: 17246 Cov.: 31 AF XY: 0.450 AC XY: 33384 AN XY: 74130

African (AFR) AF: 0.668 AC: 27646 AN: 41404

American (AMR) AF: 0.392 AC: 5977 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3466

East Asian (EAS) AF: 0.170 AC: 871 AN: 5130

South Asian (SAS) AF: 0.422 AC: 2023 AN: 4798

European-Finnish (FIN) AF: 0.325 AC: 3427 AN: 10534

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26562 AN: 67894

Other (OTH) AF: 0.453 AC: 955 AN: 2108

Alfa AF: 0.434 Hom.: 1891

Bravo AF: 0.470

Asia WGS AF: 0.336 AC: 1174 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	0.20
DANN	Benign	0.54
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6819266; hg19: chr4-63342270;