11-130931501-T-C

Variant names:

• chr11-130931501-T-C
• rs1893225

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 0.813 in 152,140 control chromosomes in the GnomAD database, including 51,078 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 0.81 (51078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 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 = 0.947 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: 0.813 AC: 123535 AN: 152024 Hom.: 51024 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.813 AC: 123643 AN: 152140 Hom.: 51078 Cov.: 31 AF XY: 0.809 AC XY: 60180 AN XY: 74372

African (AFR) AF: 0.955 AC: 39673 AN: 41552

American (AMR) AF: 0.675 AC: 10306 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3337 AN: 5162

South Asian (SAS) AF: 0.829 AC: 3981 AN: 4802

European-Finnish (FIN) AF: 0.822 AC: 8706 AN: 10590

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52428 AN: 67990

Other (OTH) AF: 0.780 AC: 1646 AN: 2110

Alfa AF: 0.793 Hom.: 8715

Bravo AF: 0.805

Asia WGS AF: 0.757 AC: 2635 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	0.10
DANN	Benign	0.67
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1893225; hg19: chr11-130801396;