rs2514531

Positions:

• chr8-96162595-G-C

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 0.346 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.346

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2514531; hg19: chr8-97174823;