rs4763299

Variant names:

• chr12-9751853-G-T
• rs4763299

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 0.163 in 151,550 control chromosomes in the GnomAD database, including 2,165 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 0.16 (2165 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 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: 0.163 AC: 24696 AN: 151432 Hom.: 2162 Cov.: 30

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.163 AC: 24710 AN: 151550 Hom.: 2165 Cov.: 30 AF XY: 0.163 AC XY: 12070 AN XY: 74034

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0136

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.155

Alfa AF: 0.180 Hom.: 2212

Bravo AF: 0.159

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4763299; hg19: chr12-9904449;