chr12-131386529-G-A

Variant names:

• chr12-131386529-G-A
• rs7976504

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 0.134 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.271 AC: 11234 AN: 41470

American (AMR) AF: 0.0740 AC: 1131 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0797 AC: 276 AN: 3462

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5176

South Asian (SAS) AF: 0.0686 AC: 330 AN: 4812

European-Finnish (FIN) AF: 0.0986 AC: 1045 AN: 10600

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6075 AN: 67994

Other (OTH) AF: 0.114 AC: 241 AN: 2106

Alfa AF: 0.107 Hom.: 347

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7976504; hg19: chr12-131871074;