rs12422191

Variant names:

• chr11-113403288-G-A
• rs12422191

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 0.0767 in 151,760 control chromosomes in the GnomAD database, including 472 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 0.077 (472 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0911 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: 0.0767 AC: 11635 AN: 151644 Hom.: 469 Cov.: 29

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.0730

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

GnomAD4 genome AF: 0.0767 AC: 11643 AN: 151760 Hom.: 472 Cov.: 29 AF XY: 0.0748 AC XY: 5550 AN XY: 74182

African (AFR) AF: 0.0566 AC: 2345 AN: 41422

American (AMR) AF: 0.0843 AC: 1286 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.0286 AC: 146 AN: 5110

South Asian (SAS) AF: 0.0310 AC: 148 AN: 4772

European-Finnish (FIN) AF: 0.0734 AC: 775 AN: 10558

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6314 AN: 67874

Other (OTH) AF: 0.0737 AC: 155 AN: 2104

Alfa AF: 0.0866 Hom.: 1720

Bravo AF: 0.0770

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.6
DANN	Benign	0.52
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12422191; hg19: chr11-113274010;