rs10519526

Variant names:

• chr4-140181050-T-A
• rs10519526

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 0.239 in 152,102 control chromosomes in the GnomAD database, including 4,470 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 0.24 (4470 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.382 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: 0.239 AC: 36310 AN: 151984 Hom.: 4452 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.239 AC: 36366 AN: 152102 Hom.: 4470 Cov.: 33 AF XY: 0.244 AC XY: 18105 AN XY: 74330

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.205

Alfa AF: 0.239 Hom.: 531

Bravo AF: 0.236

Asia WGS AF: 0.298 AC: 1035 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519526; hg19: chr4-141102204;