rs4315839

Variant names:

• chr4-183442703-T-C
• rs4315839

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 0.594 in 152,074 control chromosomes in the GnomAD database, including 30,148 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 0.59 (30148 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 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: 0.594 AC: 90330 AN: 151956 Hom.: 30130 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.594 AC: 90384 AN: 152074 Hom.: 30148 Cov.: 33 AF XY: 0.586 AC XY: 43577 AN XY: 74342

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.598

Alfa AF: 0.653 Hom.: 6663

Bravo AF: 0.564

Asia WGS AF: 0.459 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4315839; hg19: chr4-184363856;