12-71937538-C-A

Variant names:

• chr12-71937538-C-A
• rs7963803

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 0.095 in 152,068 control chromosomes in the GnomAD database, including 779 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 0.095 (779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 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: 0.0948 AC: 14407 AN: 151950 Hom.: 774 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0950 AC: 14445 AN: 152068 Hom.: 779 Cov.: 32 AF XY: 0.0963 AC XY: 7157 AN XY: 74332

African (AFR) AF: 0.136 AC: 5660 AN: 41488

American (AMR) AF: 0.0867 AC: 1325 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.167 AC: 865 AN: 5170

South Asian (SAS) AF: 0.113 AC: 542 AN: 4812

European-Finnish (FIN) AF: 0.0762 AC: 805 AN: 10560

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0717 AC: 4873 AN: 67970

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.0637 Hom.: 314

Bravo AF: 0.0972

Asia WGS AF: 0.161 AC: 560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs7963803; hg19: chr12-72331318;