chr5-25515826-A-G

Variant names:

• chr5-25515826-A-G
• rs7705483

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 0.55 in 151,964 control chromosomes in the GnomAD database, including 23,468 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 0.55 (23468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.550 AC: 83559 AN: 151846 Hom.: 23434 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.550 AC: 83641 AN: 151964 Hom.: 23468 Cov.: 32 AF XY: 0.550 AC XY: 40828 AN XY: 74262

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.548

Alfa AF: 0.518 Hom.: 40822

Bravo AF: 0.548

Asia WGS AF: 0.487 AC: 1689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705483; hg19: chr5-25515935;