5-25898812-T-C

Variant names:

• chr5-25898812-T-C
• rs7704909

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;