chr5-1248932-C-T

Variant names:

• chr5-1248932-C-T
• rs4583925

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00933 AC: 388 AN: 41588

American (AMR) AF: 0.0514 AC: 787 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0288 AC: 139 AN: 4830

European-Finnish (FIN) AF: 0.0967 AC: 1026 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4131 AN: 68022

Other (OTH) AF: 0.0388 AC: 82 AN: 2116

Alfa AF: 0.0575 Hom.: 131

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4583925; hg19: chr5-1249047;