rs4693803

Variant names:

• chr4-87147379-T-G
• rs4693803

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 0.331 in 152,046 control chromosomes in the GnomAD database, including 9,075 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 0.33 (9075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50357 AN: 151924 Hom.: 9066 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.331 AC: 50380 AN: 152046 Hom.: 9075 Cov.: 32 AF XY: 0.328 AC XY: 24388 AN XY: 74296

African (AFR) AF: 0.208 AC: 8647 AN: 41508

American (AMR) AF: 0.339 AC: 5166 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3470

East Asian (EAS) AF: 0.130 AC: 673 AN: 5170

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3808 AN: 10542

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27936 AN: 67972

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.385 Hom.: 19831

Bravo AF: 0.320

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs4693803; hg19: chr4-88068531; COSMIC: COSV70614094;