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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.569

Alfa AF: 0.444 Hom.: 34619

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6773931; hg19: chr3-56735180;