4-5002185-A-G

Variant names:

• chr4-5002185-A-G
• rs13117014

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 0.4 in 151,666 control chromosomes in the GnomAD database, including 12,382 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 0.40 (12382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.400 AC: 60583 AN: 151548 Hom.: 12343 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.400 AC: 60680 AN: 151666 Hom.: 12382 Cov.: 32 AF XY: 0.404 AC XY: 29911 AN XY: 74106

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.404

Alfa AF: 0.245 Hom.: 596

Bravo AF: 0.406

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.89
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13117014; hg19: chr4-5003912;