rs11015914

Variant names:

• chr10-27622742-C-A
• rs11015914

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 0.0963 in 152,176 control chromosomes in the GnomAD database, including 1,023 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 0.096 (1023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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: 0.0963 AC: 14649 AN: 152058 Hom.: 1028 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.0963 AC: 14662 AN: 152176 Hom.: 1023 Cov.: 33 AF XY: 0.100 AC XY: 7470 AN XY: 74388

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0660 Hom.: 212

Bravo AF: 0.105

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11015914; hg19: chr10-27911671;