11-113385786-G-A

Variant names:

• chr11-113385786-G-A
• rs877138

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 0.68 in 152,144 control chromosomes in the GnomAD database, including 35,606 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 0.68 (35606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103390 AN: 152026 Hom.: 35586 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.680 AC: 103457 AN: 152144 Hom.: 35606 Cov.: 33 AF XY: 0.676 AC XY: 50266 AN XY: 74358

African (AFR) AF: 0.777 AC: 32262 AN: 41512

American (AMR) AF: 0.582 AC: 8895 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2352 AN: 3472

East Asian (EAS) AF: 0.553 AC: 2859 AN: 5168

South Asian (SAS) AF: 0.592 AC: 2861 AN: 4832

European-Finnish (FIN) AF: 0.667 AC: 7048 AN: 10570

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44900 AN: 67992

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.665 Hom.: 57047

Bravo AF: 0.677

Asia WGS AF: 0.555 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.46
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs877138; hg19: chr11-113256508;