rs4763797

Variant names:

• chr12-12293999-G-A
• rs4763797

Your query was ambiguous. Multiple possible variants found:

• chr12-12293999-G-A
• chr12-12293999-G-C

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 0.59 in 152,026 control chromosomes in the GnomAD database, including 27,173 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 0.59 (27173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.590 AC: 89633 AN: 151908 Hom.: 27153 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.590 AC: 89680 AN: 152026 Hom.: 27173 Cov.: 32 AF XY: 0.599 AC XY: 44501 AN XY: 74296

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.591

Alfa AF: 0.605 Hom.: 13765

Bravo AF: 0.587

Asia WGS AF: 0.678 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4763797; hg19: chr12-12446933;