5-58025127-C-G

Variant names:

• chr5-58025127-C-G
• rs1844437

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 0.841 in 152,044 control chromosomes in the GnomAD database, including 54,064 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 0.84 (54064 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127808 AN: 151926 Hom.: 54008 Cov.: 31

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.841 AC: 127924 AN: 152044 Hom.: 54064 Cov.: 31 AF XY: 0.844 AC XY: 62739 AN XY: 74294

African (AFR) AF: 0.907 AC: 37636 AN: 41488

American (AMR) AF: 0.876 AC: 13374 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2816 AN: 3464

East Asian (EAS) AF: 0.848 AC: 4384 AN: 5172

South Asian (SAS) AF: 0.916 AC: 4417 AN: 4824

European-Finnish (FIN) AF: 0.816 AC: 8583 AN: 10522

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53975 AN: 67986

Other (OTH) AF: 0.822 AC: 1737 AN: 2112

Alfa AF: 0.826 Hom.: 6074

Bravo AF: 0.845

Asia WGS AF: 0.873 AC: 3023 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.45
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs1844437; hg19: chr5-57320954;