11-116736721-C-T

Variant names:

• chr11-116736721-C-T
• rs1558861

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 0.927 in 152,246 control chromosomes in the GnomAD database, including 65,754 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 0.93 (65754 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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: 0.928 AC: 141104 AN: 152128 Hom.: 65706 Cov.: 31

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.927 AC: 141208 AN: 152246 Hom.: 65754 Cov.: 31 AF XY: 0.923 AC XY: 68717 AN XY: 74432

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.918

Alfa AF: 0.931 Hom.: 21567

Bravo AF: 0.927

Asia WGS AF: 0.799 AC: 2782 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	1.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558861; hg19: chr11-116607437;