rs12270338

chr11-94414298-C-Achr11-94414298-C-G

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.182

Alfa AF: 0.200 Hom.: 3732

Bravo AF: 0.186

Asia WGS AF: 0.192 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12270338; hg19: chr11-94147464;