chr6-31515638-C-A

Variant names:

• chr6-31515638-C-A
• rs2844494

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 0.699 in 152,064 control chromosomes in the GnomAD database, including 37,346 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 0.70 (37346 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106267 AN: 151946 Hom.: 37317 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.699 AC: 106344 AN: 152064 Hom.: 37346 Cov.: 31 AF XY: 0.703 AC XY: 52230 AN XY: 74324

African (AFR) AF: 0.740 AC: 30677 AN: 41470

American (AMR) AF: 0.638 AC: 9752 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2868 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3828 AN: 5174

South Asian (SAS) AF: 0.726 AC: 3494 AN: 4814

European-Finnish (FIN) AF: 0.763 AC: 8079 AN: 10584

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45346 AN: 67946

Other (OTH) AF: 0.696 AC: 1469 AN: 2112

Alfa AF: 0.682 Hom.: 88845

Bravo AF: 0.690

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs2844494; hg19: chr6-31483415;