chr5-25898812-T-C

Position:

• chr5-25898812-T-C

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 0.278 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.303

Alfa AF: 0.358 Hom.: 13361

Bravo AF: 0.260

Asia WGS AF: 0.244 AC: 846 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7704909; hg19: chr5-25898921;