rs4763299

Variant names:

• chr12-9751853-G-T
• rs4763299

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 0.163 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.139 AC: 5749 AN: 41316

American (AMR) AF: 0.170 AC: 2584 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3468

East Asian (EAS) AF: 0.0136 AC: 70 AN: 5148

South Asian (SAS) AF: 0.0943 AC: 452 AN: 4792

European-Finnish (FIN) AF: 0.203 AC: 2130 AN: 10478

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12573 AN: 67866

Other (OTH) AF: 0.155 AC: 325 AN: 2100

Alfa AF: 0.177 Hom.: 2882

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs4763299; hg19: chr12-9904449;