rs2596517

chr6-31392318-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;