rs2596530

Variant names:

• chr6-31419596-G-A
• rs2596530
• ENST00000673857.1:n.62+18833G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.62+18833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,702 control chromosomes in the GnomAD database, including 32,226 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 0.64 (32226 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 29 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 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
ENSG00000288587	ENST00000673857.1	n.62+18833G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97163 AN: 151584 Hom.: 32181 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.641 AC: 97264 AN: 151702 Hom.: 32226 Cov.: 32 AF XY: 0.652 AC XY: 48367 AN XY: 74200

African (AFR) AF: 0.703 AC: 28988 AN: 41232

American (AMR) AF: 0.781 AC: 11870 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2845 AN: 3462

East Asian (EAS) AF: 0.786 AC: 4047 AN: 5150

South Asian (SAS) AF: 0.797 AC: 3843 AN: 4824

European-Finnish (FIN) AF: 0.601 AC: 6349 AN: 10564

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

European-Non Finnish (NFE) AF: 0.545 AC: 37054 AN: 67952

Other (OTH) AF: 0.726 AC: 1531 AN: 2108

Alfa AF: 0.597 Hom.: 49626

Bravo AF: 0.658

Asia WGS AF: 0.821 AC: 2853 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2596530; hg19: chr6-31387373;