13-25214448-T-C

Position:

• chr13-25214448-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 0.666 in 151,884 control chromosomes in the GnomAD database, including 34,949 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 0.67 (34949 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 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: 0.666 AC: 101032 AN: 151766 Hom.: 34926 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.666 AC: 101090 AN: 151884 Hom.: 34949 Cov.: 30 AF XY: 0.662 AC XY: 49155 AN XY: 74250

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.680

Alfa AF: 0.747 Hom.: 52658

Bravo AF: 0.638

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.53
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4769414; hg19: chr13-25788586; COSMIC: COSV71236728;