4-3764028-C-T

Variant names:

• chr4-3764028-C-T
• rs13118771

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 0.873 in 152,182 control chromosomes in the GnomAD database, including 58,287 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 0.87 (58287 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.873 AC: 132738 AN: 152064 Hom.: 58240 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.873 AC: 132840 AN: 152182 Hom.: 58287 Cov.: 33 AF XY: 0.868 AC XY: 64581 AN XY: 74382

African (AFR) AF: 0.899 AC: 37381 AN: 41564

American (AMR) AF: 0.798 AC: 12202 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3062 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3174 AN: 5122

South Asian (SAS) AF: 0.778 AC: 3757 AN: 4828

European-Finnish (FIN) AF: 0.883 AC: 9374 AN: 10614

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60929 AN: 67970

Other (OTH) AF: 0.884 AC: 1870 AN: 2116

Alfa AF: 0.883 Hom.: 113410

Bravo AF: 0.868

Asia WGS AF: 0.713 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.056
DANN	Benign	0.26
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13118771; hg19: chr4-3765755;