rs10515322

Variant names:

• chr5-102175940-A-T
• rs10515322

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 0.331 in 151,858 control chromosomes in the GnomAD database, including 8,891 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 0.33 (8891 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.331 AC: 50167 AN: 151740 Hom.: 8873 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.331 AC: 50226 AN: 151858 Hom.: 8891 Cov.: 31 AF XY: 0.329 AC XY: 24403 AN XY: 74220

African (AFR) AF: 0.458 AC: 18978 AN: 41396

American (AMR) AF: 0.277 AC: 4222 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4810

European-Finnish (FIN) AF: 0.243 AC: 2552 AN: 10516

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19421 AN: 67928

Other (OTH) AF: 0.298 AC: 629 AN: 2110

Alfa AF: 0.312 Hom.: 938

Bravo AF: 0.340

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.0
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10515322; hg19: chr5-101511644;