rs1150226

chr11-113974819-A-Gchr11-113974819-A-T

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 0.892 in 287,354 control chromosomes in the GnomAD database, including 115,756 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 0.86 (57429 hom., cov: 29)
  • Exomes 𝑓: 0.93 (58327 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130861 AN: 151792 Hom.: 57406 Cov.: 29

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.877

GnomAD4 exome AF: 0.926 AC: 125441 AN: 135448 Hom.: 58327 AF XY: 0.929 AC XY: 66235 AN XY: 71298

Gnomad4 AFR exome AF: 0.663

Gnomad4 AMR exome AF: 0.926

Gnomad4 ASJ exome AF: 0.972

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.955

Gnomad4 FIN exome AF: 0.966

Gnomad4 NFE exome AF: 0.922

Gnomad4 OTH exome AF: 0.924

GnomAD4 genome AF: 0.862 AC: 130935 AN: 151906 Hom.: 57429 Cov.: 29 AF XY: 0.867 AC XY: 64371 AN XY: 74230

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.878

Alfa AF: 0.906 Hom.: 84713

Bravo AF: 0.850

Asia WGS AF: 0.964 AC: 3354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.48
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150226; hg19: chr11-113845541;