rs2857596

Variant names:

• chr6-31599645-G-T
• rs2857596

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 0.787 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.787 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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.804

Alfa AF: 0.760 Hom.: 26222

Bravo AF: 0.784

Asia WGS AF: 0.843 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857596; hg19: chr6-31567422;