rs3134782

Variant names:

• chr6-31229856-G-A
• rs3134782

Your query was ambiguous. Multiple possible variants found:

• chr6-31229856-G-A
• chr6-31229856-G-C
• chr6-31229856-G-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 0.871 in 151,958 control chromosomes in the GnomAD database, including 57,841 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 0.87 (57841 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 25 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 (AFR) allele frequency at 95% confidence interval = 0.923 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: 0.871 AC: 132323 AN: 151840 Hom.: 57789 Cov.: 28

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.933

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.871 AC: 132430 AN: 151958 Hom.: 57841 Cov.: 28 AF XY: 0.870 AC XY: 64623 AN XY: 74250

African (AFR) AF: 0.931 AC: 38584 AN: 41464

American (AMR) AF: 0.866 AC: 13211 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3177 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4163 AN: 5144

South Asian (SAS) AF: 0.792 AC: 3816 AN: 4816

European-Finnish (FIN) AF: 0.850 AC: 8976 AN: 10558

Middle Eastern (MID) AF: 0.932 AC: 272 AN: 292

European-Non Finnish (NFE) AF: 0.847 AC: 57567 AN: 67940

Other (OTH) AF: 0.894 AC: 1887 AN: 2110

Alfa AF: 0.870 Hom.: 130959

Bravo AF: 0.879

Asia WGS AF: 0.843 AC: 2934 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	3.0
DANN	Benign	0.33
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3134782; hg19: chr6-31197633;