rs4768736

Variant names:

• chr12-39291731-G-A
• rs4768736

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 0.0679 in 152,282 control chromosomes in the GnomAD database, including 721 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 0.068 (721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 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: 0.0679 AC: 10330 AN: 152164 Hom.: 719 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0679 AC: 10342 AN: 152282 Hom.: 721 Cov.: 32 AF XY: 0.0710 AC XY: 5289 AN XY: 74468

African (AFR) AF: 0.0162 AC: 675 AN: 41554

American (AMR) AF: 0.188 AC: 2884 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1609 AN: 5182

South Asian (SAS) AF: 0.0557 AC: 269 AN: 4826

European-Finnish (FIN) AF: 0.0682 AC: 723 AN: 10608

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3691 AN: 68018

Other (OTH) AF: 0.0922 AC: 195 AN: 2116

Alfa AF: 0.0684 Hom.: 878

Bravo AF: 0.0796

Asia WGS AF: 0.173 AC: 598 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4768736; hg19: chr12-39685533;