rs4693803

Variant names:

• chr4-87147379-T-G
• rs4693803

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.331 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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.330

Alfa AF: 0.392 Hom.: 16238

Bravo AF: 0.320

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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