rs4583925

Variant names:

• chr5-1248932-C-T
• rs4583925

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 0.0441 in 152,338 control chromosomes in the GnomAD database, including 226 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 0.044 (226 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

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 (NFE) allele frequency at 95% confidence interval = 0.0592 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: 0.0441 AC: 6718 AN: 152220 Hom.: 226 Cov.: 33

Gnomad AFR AF: 0.00936

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0285

Gnomad FIN AF: 0.0967

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0441 AC: 6724 AN: 152338 Hom.: 226 Cov.: 33 AF XY: 0.0452 AC XY: 3366 AN XY: 74490

Gnomad4 AFR AF: 0.00933

Gnomad4 AMR AF: 0.0514

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0288

Gnomad4 FIN AF: 0.0967

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0590 Hom.: 88

Bravo AF: 0.0407

Asia WGS AF: 0.0230 AC: 81 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	3.9
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: rs4583925; hg19: chr5-1249047;