rs10815188

Variant names:

• chr9-5354681-C-T
• rs10815188

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 0.476 in 151,978 control chromosomes in the GnomAD database, including 17,628 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 0.48 (17628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.476 AC: 72240 AN: 151860 Hom.: 17608 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.476 AC: 72309 AN: 151978 Hom.: 17628 Cov.: 32 AF XY: 0.479 AC XY: 35560 AN XY: 74278

African (AFR) AF: 0.589 AC: 24415 AN: 41472

American (AMR) AF: 0.487 AC: 7435 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1699 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2470 AN: 5166

South Asian (SAS) AF: 0.472 AC: 2278 AN: 4826

European-Finnish (FIN) AF: 0.428 AC: 4508 AN: 10534

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28057 AN: 67940

Other (OTH) AF: 0.494 AC: 1040 AN: 2106

Alfa AF: 0.443 Hom.: 19836

Bravo AF: 0.485

Asia WGS AF: 0.523 AC: 1819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.58
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10815188; hg19: chr9-5354681;