13-25150931-C-T

Position:

• chr13-25150931-C-T

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 0.136 in 152,154 control chromosomes in the GnomAD database, including 1,542 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 0.14 (1542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20704 AN: 152038 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.136 AC: 20720 AN: 152154 Hom.: 1542 Cov.: 32 AF XY: 0.141 AC XY: 10485 AN XY: 74364

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.149

Alfa AF: 0.129 Hom.: 1963

Bravo AF: 0.138

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507344; hg19: chr13-25725069;