rs12270115

Variant names:

• chr11-79774093-G-A
• rs12270115

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 0.167 in 152,250 control chromosomes in the GnomAD database, including 2,693 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 0.17 (2693 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.167 AC: 25409 AN: 152132 Hom.: 2688 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.167 AC: 25435 AN: 152250 Hom.: 2693 Cov.: 33 AF XY: 0.165 AC XY: 12252 AN XY: 74440

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.153

Alfa AF: 0.139 Hom.: 1637

Bravo AF: 0.172

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.3
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: rs12270115; hg19: chr11-79485137;