rs4583925

Positions:

• chr5-1248932-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 0.0441 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;