12-57229038-G-A

Variant names:

• chr12-57229038-G-A
• rs7301155

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 0.679 in 151,932 control chromosomes in the GnomAD database, including 35,216 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 0.68 (35216 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103051 AN: 151814 Hom.: 35184 Cov.: 30

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.679 AC: 103129 AN: 151932 Hom.: 35216 Cov.: 30 AF XY: 0.678 AC XY: 50330 AN XY: 74226

African (AFR) AF: 0.723 AC: 29933 AN: 41424

American (AMR) AF: 0.619 AC: 9447 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2277 AN: 3470

East Asian (EAS) AF: 0.577 AC: 2975 AN: 5156

South Asian (SAS) AF: 0.762 AC: 3660 AN: 4800

European-Finnish (FIN) AF: 0.648 AC: 6820 AN: 10530

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45877 AN: 67972

Other (OTH) AF: 0.664 AC: 1400 AN: 2110

Alfa AF: 0.663 Hom.: 21870

Bravo AF: 0.667

Asia WGS AF: 0.643 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.62
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7301155; hg19: chr12-57622821;