chr6-31229737-C-G

Variant names:

• chr6-31229737-C-G
• rs3130941

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 0.872 in 152,244 control chromosomes in the GnomAD database, including 58,047 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 (58047 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132672 AN: 152126 Hom.: 57993 Cov.: 31

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.872 AC: 132781 AN: 152244 Hom.: 58047 Cov.: 31 AF XY: 0.871 AC XY: 64826 AN XY: 74430

African (AFR) AF: 0.933 AC: 38747 AN: 41538

American (AMR) AF: 0.867 AC: 13263 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3175 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4190 AN: 5174

South Asian (SAS) AF: 0.793 AC: 3825 AN: 4826

European-Finnish (FIN) AF: 0.850 AC: 9010 AN: 10600

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57628 AN: 68014

Other (OTH) AF: 0.895 AC: 1892 AN: 2114

Alfa AF: 0.858 Hom.: 6967

Bravo AF: 0.879

Asia WGS AF: 0.844 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.36
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs3130941; hg19: chr6-31197514;