5-25885557-G-T

Variant names:

• chr5-25885557-G-T
• rs731999

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 0.387 in 151,554 control chromosomes in the GnomAD database, including 11,635 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 0.39 (11635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.387 AC: 58554 AN: 151436 Hom.: 11625 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.387 AC: 58595 AN: 151554 Hom.: 11635 Cov.: 32 AF XY: 0.387 AC XY: 28617 AN XY: 74032

African (AFR) AF: 0.392 AC: 16174 AN: 41284

American (AMR) AF: 0.481 AC: 7318 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2715 AN: 5148

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2777 AN: 10444

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25011 AN: 67866

Other (OTH) AF: 0.423 AC: 892 AN: 2110

Alfa AF: 0.370 Hom.: 2136

Bravo AF: 0.402

Asia WGS AF: 0.477 AC: 1653 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.21
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs731999; hg19: chr5-25885666;