rs10515535

Variant names:

• chr5-144136577-A-G
• rs10515535

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 0.462 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.184 AC: 7644 AN: 41482

American (AMR) AF: 0.534 AC: 8135 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2277 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2576 AN: 5160

South Asian (SAS) AF: 0.480 AC: 2313 AN: 4820

European-Finnish (FIN) AF: 0.577 AC: 6090 AN: 10558

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39518 AN: 67974

Other (OTH) AF: 0.485 AC: 1020 AN: 2102

Alfa AF: 0.555 Hom.: 14818

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs10515535; hg19: chr5-143516142;