11-130931501-T-C

Variant names:

• chr11-130931501-T-C
• rs1893225

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 0.813 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.813 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

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.780

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893225; hg19: chr11-130801396;