rs2596517

Variant names:

• chr6-31392318-G-A
• rs2596517

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 0.848 in 151,740 control chromosomes in the GnomAD database, including 54,869 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 0.85 (54869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 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: 0.848 AC: 128638 AN: 151624 Hom.: 54817 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.848 AC: 128745 AN: 151740 Hom.: 54869 Cov.: 32 AF XY: 0.852 AC XY: 63197 AN XY: 74146

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.882

Alfa AF: 0.833 Hom.: 7167

Bravo AF: 0.850

Asia WGS AF: 0.936 AC: 3252 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596517; hg19: chr6-31360095;