chr12-131386529-G-A

Position:

• chr12-131386529-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 0.134 in 152,112 control chromosomes in the GnomAD database, including 1,947 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 0.13 (1947 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20358 AN: 151994 Hom.: 1944 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0797

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0986

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.134 AC: 20381 AN: 152112 Hom.: 1947 Cov.: 33 AF XY: 0.131 AC XY: 9716 AN XY: 74370

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.0797

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0986

Gnomad4 NFE AF: 0.0893

Gnomad4 OTH AF: 0.114

Alfa AF: 0.105 Hom.: 206

Bravo AF: 0.138

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.50
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7976504; hg19: chr12-131871074;