5-25841504-G-A

Position:

• chr5-25841504-G-A

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 0.295 in 151,778 control chromosomes in the GnomAD database, including 7,087 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 0.30 (7087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

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 (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.295 AC: 44815 AN: 151660 Hom.: 7085 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.295 AC: 44841 AN: 151778 Hom.: 7087 Cov.: 32 AF XY: 0.298 AC XY: 22129 AN XY: 74152

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.314

Alfa AF: 0.349 Hom.: 16058

Bravo AF: 0.285

Asia WGS AF: 0.286 AC: 993 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs396045; hg19: chr5-25841613;