rs10515081

Variant names:

• chr5-68364812-G-A
• rs10515081

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 0.0483 in 152,110 control chromosomes in the GnomAD database, including 257 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 0.048 (257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0875 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: 0.0483 AC: 7348 AN: 151990 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0483 AC: 7354 AN: 152110 Hom.: 257 Cov.: 32 AF XY: 0.0498 AC XY: 3700 AN XY: 74350

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0532 Hom.: 98

Bravo AF: 0.0468

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515081; hg19: chr5-67660640; COSMIC: COSV60151293;