rs6773931

Variant names:

• chr3-56701152-C-A
• rs6773931

Your query was ambiguous. Multiple possible variants found:

• chr3-56701152-C-A
• chr3-56701152-C-G
• chr3-56701152-C-T

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 0.574 in 151,984 control chromosomes in the GnomAD database, including 27,666 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 0.57 (27666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.574 AC: 87114 AN: 151866 Hom.: 27599 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.574 AC: 87244 AN: 151984 Hom.: 27666 Cov.: 32 AF XY: 0.581 AC XY: 43155 AN XY: 74274

African (AFR) AF: 0.812 AC: 33665 AN: 41484

American (AMR) AF: 0.647 AC: 9878 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1370 AN: 3462

East Asian (EAS) AF: 0.863 AC: 4465 AN: 5172

South Asian (SAS) AF: 0.721 AC: 3481 AN: 4828

European-Finnish (FIN) AF: 0.464 AC: 4884 AN: 10518

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27699 AN: 67942

Other (OTH) AF: 0.569 AC: 1202 AN: 2112

Alfa AF: 0.467 Hom.: 82556

Bravo AF: 0.598

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6773931; hg19: chr3-56735180;