rs11015914

Variant names:

• chr10-27622742-C-A
• rs11015914

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 0.0963 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.122 AC: 5043 AN: 41506

American (AMR) AF: 0.159 AC: 2430 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1689 AN: 5176

South Asian (SAS) AF: 0.119 AC: 575 AN: 4824

European-Finnish (FIN) AF: 0.0993 AC: 1052 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3396 AN: 68010

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0659 Hom.: 235

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11015914; hg19: chr10-27911671;