chr5-25515826-A-G

Variant names:

• chr5-25515826-A-G
• rs7705483

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 0.55 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.655 AC: 27149 AN: 41440

American (AMR) AF: 0.502 AC: 7661 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3466

East Asian (EAS) AF: 0.327 AC: 1677 AN: 5132

South Asian (SAS) AF: 0.565 AC: 2726 AN: 4824

European-Finnish (FIN) AF: 0.560 AC: 5924 AN: 10570

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.517 AC: 35148 AN: 67962

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

Alfa AF: 0.526 Hom.: 66837

Bravo AF: 0.548

Asia WGS AF: 0.487 AC: 1689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7705483; hg19: chr5-25515935;