rs4763299

chr12-9751853-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;