chr4-3763742-C-T

Variant names:

• chr4-3763742-C-T
• rs9790683

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 152,140 control chromosomes in the GnomAD database, including 58,293 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 (58293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 132730 AN: 152022 Hom.: 58246 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.873 AC: 132832 AN: 152140 Hom.: 58293 Cov.: 32 AF XY: 0.868 AC XY: 64588 AN XY: 74374

African (AFR) AF: 0.900 AC: 37401 AN: 41544

American (AMR) AF: 0.797 AC: 12200 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3059 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3171 AN: 5116

South Asian (SAS) AF: 0.781 AC: 3768 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9361 AN: 10610

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

European-Non Finnish (NFE) AF: 0.896 AC: 60913 AN: 67954

Other (OTH) AF: 0.884 AC: 1866 AN: 2112

Alfa AF: 0.892 Hom.: 8905

Bravo AF: 0.868

Asia WGS AF: 0.714 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9790683; hg19: chr4-3765469;