chr12-115132241-G-A

Position:

• chr12-115132241-G-A

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 0.692 in 152,090 control chromosomes in the GnomAD database, including 38,174 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 0.69 (38174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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: 0.691 AC: 105083 AN: 151972 Hom.: 38101 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.692 AC: 105213 AN: 152090 Hom.: 38174 Cov.: 32 AF XY: 0.689 AC XY: 51213 AN XY: 74328

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.675

Alfa AF: 0.603 Hom.: 40795

Bravo AF: 0.704

Asia WGS AF: 0.734 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
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: rs35426; hg19: chr12-115570046;