rs10962015

Variant names:

• chr9-15387951-G-A
• rs10962015

Your query was ambiguous. Multiple possible variants found:

• chr9-15387951-G-A
• chr9-15387951-G-T

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 0.18 in 152,104 control chromosomes in the GnomAD database, including 2,806 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 0.18 (2806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.180 AC: 27399 AN: 151986 Hom.: 2800 Cov.: 32

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.180 AC: 27415 AN: 152104 Hom.: 2806 Cov.: 32 AF XY: 0.179 AC XY: 13333 AN XY: 74362

African (AFR) AF: 0.0808 AC: 3355 AN: 41502

American (AMR) AF: 0.204 AC: 3109 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.137 AC: 708 AN: 5172

South Asian (SAS) AF: 0.171 AC: 825 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2025 AN: 10578

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15970 AN: 67974

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.207 Hom.: 11980

Bravo AF: 0.176

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10962015; hg19: chr9-15387949;