chr12-94726040-T-C

Variant names:

• chr12-94726040-T-C
• rs7302717

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 0.711 in 152,014 control chromosomes in the GnomAD database, including 39,007 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 0.71 (39007 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 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: 0.712 AC: 108081 AN: 151896 Hom.: 38993 Cov.: 30

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.711 AC: 108131 AN: 152014 Hom.: 39007 Cov.: 30 AF XY: 0.710 AC XY: 52724 AN XY: 74292

African (AFR) AF: 0.587 AC: 24324 AN: 41420

American (AMR) AF: 0.790 AC: 12077 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2495 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3747 AN: 5172

South Asian (SAS) AF: 0.721 AC: 3476 AN: 4818

European-Finnish (FIN) AF: 0.730 AC: 7712 AN: 10558

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51864 AN: 67976

Other (OTH) AF: 0.721 AC: 1523 AN: 2112

Alfa AF: 0.750 Hom.: 61193

Bravo AF: 0.711

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7302717; hg19: chr12-95119816;