rs10515535

Variant names:

• chr5-144136577-A-G
• rs10515535

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 0.462 in 152,018 control chromosomes in the GnomAD database, including 18,581 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 0.46 (18581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 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: 0.462 AC: 70229 AN: 151898 Hom.: 18586 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.462 AC: 70239 AN: 152018 Hom.: 18581 Cov.: 32 AF XY: 0.464 AC XY: 34471 AN XY: 74288

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.485

Alfa AF: 0.558 Hom.: 13518

Bravo AF: 0.454

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515535; hg19: chr5-143516142;