4-5002185-A-G

Position:

• chr4-5002185-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;