12-131386480-C-T

Variant names:

• chr12-131386480-C-T
• rs7977251

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 0.124 in 152,226 control chromosomes in the GnomAD database, including 1,556 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 0.12 (1556 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 4 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 = 0.233 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18840 AN: 152108 Hom.: 1553 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.124 AC: 18862 AN: 152226 Hom.: 1556 Cov.: 33 AF XY: 0.121 AC XY: 8998 AN XY: 74432

African (AFR) AF: 0.237 AC: 9844 AN: 41512

American (AMR) AF: 0.0710 AC: 1087 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0796 AC: 276 AN: 3466

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4820

European-Finnish (FIN) AF: 0.0978 AC: 1038 AN: 10614

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0885 AC: 6019 AN: 68010

Other (OTH) AF: 0.106 AC: 224 AN: 2114

Alfa AF: 0.0868 Hom.: 708

Bravo AF: 0.127

Asia WGS AF: 0.0410 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7977251; hg19: chr12-131871025;