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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.590 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

African (AFR) AF: 0.452 AC: 18749 AN: 41466

American (AMR) AF: 0.725 AC: 11073 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3468

East Asian (EAS) AF: 0.739 AC: 3822 AN: 5174

South Asian (SAS) AF: 0.665 AC: 3211 AN: 4830

European-Finnish (FIN) AF: 0.696 AC: 7338 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41545 AN: 67960

Other (OTH) AF: 0.591 AC: 1245 AN: 2108

Alfa AF: 0.604 Hom.: 18567

Bravo AF: 0.587

Asia WGS AF: 0.678 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.6
DANN	Benign	0.72
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs4763797; hg19: chr12-12446933;