5-25898812-T-C

Variant names:

• chr5-25898812-T-C
• rs7704909

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 0.278 in 151,930 control chromosomes in the GnomAD database, including 7,445 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 0.28 (7445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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: 0.279 AC: 42288 AN: 151814 Hom.: 7445 Cov.: 32

Gnomad AFR AF: 0.0705

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.278 AC: 42286 AN: 151930 Hom.: 7445 Cov.: 32 AF XY: 0.280 AC XY: 20798 AN XY: 74262

African (AFR) AF: 0.0704 AC: 2919 AN: 41492

American (AMR) AF: 0.275 AC: 4200 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3472

East Asian (EAS) AF: 0.151 AC: 778 AN: 5152

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4390 AN: 10502

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.379 AC: 25766 AN: 67924

Other (OTH) AF: 0.303 AC: 636 AN: 2102

Alfa AF: 0.348 Hom.: 16309

Bravo AF: 0.260

Asia WGS AF: 0.244 AC: 846 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.45
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs7704909; hg19: chr5-25898921;