12-71937538-C-A

Variant names:

• chr12-71937538-C-A
• rs7963803

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0948 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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0762

Gnomad4 NFE AF: 0.0717

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0610 Hom.: 243

Bravo AF: 0.0972

Asia WGS AF: 0.161 AC: 560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7963803; hg19: chr12-72331318;