rs2857596

Variant names:

• chr6-31599645-G-T
• rs2857596

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 0.787 in 151,098 control chromosomes in the GnomAD database, including 46,969 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 0.79 (46969 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.787 AC: 118831 AN: 150980 Hom.: 46901 Cov.: 28

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.787 AC: 118961 AN: 151098 Hom.: 46969 Cov.: 28 AF XY: 0.794 AC XY: 58558 AN XY: 73756

African (AFR) AF: 0.802 AC: 33016 AN: 41142

American (AMR) AF: 0.805 AC: 12183 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3033 AN: 3464

East Asian (EAS) AF: 0.912 AC: 4719 AN: 5174

South Asian (SAS) AF: 0.904 AC: 4333 AN: 4794

European-Finnish (FIN) AF: 0.806 AC: 8335 AN: 10342

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50638 AN: 67746

Other (OTH) AF: 0.804 AC: 1692 AN: 2104

Alfa AF: 0.760 Hom.: 49837

Bravo AF: 0.784

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.055
DANN	Benign	0.33
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2857596; hg19: chr6-31567422;