rs10515322

Positions:

• chr5-102175940-A-T

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 0.331 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.298

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515322; hg19: chr5-101511644;