11-111326133-T-C

Variant names:

• chr11-111326133-T-C
• rs7104791

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 0.743 in 151,940 control chromosomes in the GnomAD database, including 42,541 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 0.74 (42541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112792 AN: 151822 Hom.: 42523 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.743 AC: 112867 AN: 151940 Hom.: 42541 Cov.: 31 AF XY: 0.735 AC XY: 54616 AN XY: 74272

African (AFR) AF: 0.719 AC: 29779 AN: 41408

American (AMR) AF: 0.816 AC: 12468 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2774 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2124 AN: 5150

South Asian (SAS) AF: 0.532 AC: 2555 AN: 4806

European-Finnish (FIN) AF: 0.704 AC: 7419 AN: 10538

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53119 AN: 67982

Other (OTH) AF: 0.782 AC: 1651 AN: 2112

Alfa AF: 0.768 Hom.: 194548

Bravo AF: 0.753

Asia WGS AF: 0.460 AC: 1602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.48
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7104791; hg19: chr11-111196858;