rs6765337

Variant names:

• chr3-176939674-T-C
• rs6765337

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 0.0916 in 152,284 control chromosomes in the GnomAD database, including 734 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 0.092 (734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 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: 0.0916 AC: 13933 AN: 152166 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0916 AC: 13949 AN: 152284 Hom.: 734 Cov.: 32 AF XY: 0.0891 AC XY: 6632 AN XY: 74462

African (AFR) AF: 0.136 AC: 5634 AN: 41550

American (AMR) AF: 0.0729 AC: 1115 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.0671 AC: 348 AN: 5188

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4826

European-Finnish (FIN) AF: 0.0585 AC: 621 AN: 10610

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5254 AN: 68026

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.0806 Hom.: 296

Bravo AF: 0.0956

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.32
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs6765337; hg19: chr3-176657462;