6-32773965-A-G

Variant names:

• chr6-32773965-A-G
• rs2857210

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 0.697 in 152,014 control chromosomes in the GnomAD database, including 37,076 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 0.70 (37076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 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: 0.698 AC: 105957 AN: 151896 Hom.: 37061 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.697 AC: 106017 AN: 152014 Hom.: 37076 Cov.: 31 AF XY: 0.702 AC XY: 52167 AN XY: 74308

African (AFR) AF: 0.666 AC: 27618 AN: 41464

American (AMR) AF: 0.694 AC: 10595 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3783 AN: 5174

South Asian (SAS) AF: 0.737 AC: 3547 AN: 4816

European-Finnish (FIN) AF: 0.789 AC: 8326 AN: 10556

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47262 AN: 67950

Other (OTH) AF: 0.697 AC: 1469 AN: 2108

Alfa AF: 0.697 Hom.: 91735

Bravo AF: 0.687

Asia WGS AF: 0.754 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.47
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs2857210; hg19: chr6-32741742; COSMIC: COSV54964685;