rs12270338

Variant names:

• chr11-94414298-C-A
• rs12270338

Your query was ambiguous. Multiple possible variants found:

• chr11-94414298-C-A
• chr11-94414298-C-G

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 0.189 in 151,790 control chromosomes in the GnomAD database, including 2,826 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 0.19 (2826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28673 AN: 151672 Hom.: 2824 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.189 AC: 28702 AN: 151790 Hom.: 2826 Cov.: 32 AF XY: 0.186 AC XY: 13811 AN XY: 74162

African (AFR) AF: 0.154 AC: 6386 AN: 41422

American (AMR) AF: 0.150 AC: 2290 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3460

East Asian (EAS) AF: 0.228 AC: 1175 AN: 5158

South Asian (SAS) AF: 0.155 AC: 748 AN: 4812

European-Finnish (FIN) AF: 0.205 AC: 2148 AN: 10492

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14823 AN: 67894

Other (OTH) AF: 0.182 AC: 383 AN: 2108

Alfa AF: 0.200 Hom.: 4576

Bravo AF: 0.186

Asia WGS AF: 0.192 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs12270338; hg19: chr11-94147464;