rs4912474

Positions:

• chr3-184148698-C-A
• chr3-184148698-C-T

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 0.348 in 152,044 control chromosomes in the GnomAD database, including 9,484 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 0.35 (9484 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.184148698C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52827 AN: 151926 Hom.: 9468 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.348 AC: 52872 AN: 152044 Hom.: 9484 Cov.: 32 AF XY: 0.349 AC XY: 25968 AN XY: 74312

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.337

Alfa AF: 0.334 Hom.: 17407

Bravo AF: 0.345

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4912474; hg19: chr3-183866486;