chr5-25885557-G-T

Position:

• chr5-25885557-G-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 0.387 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.423

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731999; hg19: chr5-25885666;