rs2514531

Variant names:

• chr8-96162595-G-C
• rs2514531

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 0.346 in 152,072 control chromosomes in the GnomAD database, including 11,073 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 0.35 (11073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 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: 0.346 AC: 52540 AN: 151954 Hom.: 11078 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.346 AC: 52541 AN: 152072 Hom.: 11073 Cov.: 32 AF XY: 0.348 AC XY: 25841 AN XY: 74316

African (AFR) AF: 0.117 AC: 4868 AN: 41494

American (AMR) AF: 0.284 AC: 4336 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5180

South Asian (SAS) AF: 0.458 AC: 2203 AN: 4806

European-Finnish (FIN) AF: 0.484 AC: 5114 AN: 10558

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32241 AN: 67964

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.414 Hom.: 1825

Bravo AF: 0.315

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2514531; hg19: chr8-97174823;