chr11-130924460-A-C

Variant names:

• chr11-130924460-A-C
• rs11222395

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 0.397 in 151,962 control chromosomes in the GnomAD database, including 13,210 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 0.40 (13210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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: 0.398 AC: 60392 AN: 151844 Hom.: 13212 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.397 AC: 60403 AN: 151962 Hom.: 13210 Cov.: 32 AF XY: 0.398 AC XY: 29555 AN XY: 74250

African (AFR) AF: 0.215 AC: 8900 AN: 41460

American (AMR) AF: 0.411 AC: 6272 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2567 AN: 5150

South Asian (SAS) AF: 0.596 AC: 2862 AN: 4802

European-Finnish (FIN) AF: 0.437 AC: 4602 AN: 10532

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32440 AN: 67958

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.457 Hom.: 10865

Bravo AF: 0.387

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.35
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs11222395; hg19: chr11-130794355;