rs10515535

chr5-144136577-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;