13-25214448-T-C

Variant names:

• chr13-25214448-T-C
• rs4769414

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;