rs4583752

Positions:

• chr4-15697382-A-G
• chr4-15697382-A-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 0.289 in 152,018 control chromosomes in the GnomAD database, including 6,589 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 0.29 (6589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43945 AN: 151900 Hom.: 6578 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.289 AC: 43981 AN: 152018 Hom.: 6589 Cov.: 32 AF XY: 0.293 AC XY: 21760 AN XY: 74290

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.308

Alfa AF: 0.293 Hom.: 8860

Bravo AF: 0.288

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4583752; hg19: chr4-15699005;