rs11015914

Positions:

• chr10-27622742-C-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;