rs6772676

Variant names:

• chr3-172467868-G-A
• rs6772676

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 0.549 in 151,752 control chromosomes in the GnomAD database, including 23,207 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 0.55 (23207 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.548 AC: 83166 AN: 151634 Hom.: 23181 Cov.: 30

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.549 AC: 83243 AN: 151752 Hom.: 23207 Cov.: 30 AF XY: 0.546 AC XY: 40438 AN XY: 74112

African (AFR) AF: 0.644 AC: 26675 AN: 41392

American (AMR) AF: 0.485 AC: 7398 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1933 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5164

South Asian (SAS) AF: 0.592 AC: 2843 AN: 4800

European-Finnish (FIN) AF: 0.521 AC: 5444 AN: 10452

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35215 AN: 67920

Other (OTH) AF: 0.548 AC: 1155 AN: 2108

Alfa AF: 0.579 Hom.: 5790

Bravo AF: 0.546

Asia WGS AF: 0.527 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6772676; hg19: chr3-172185658;