chr13-26796532-C-T

Variant names:

• chr13-26796532-C-T
• rs2182880

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 0.444 in 152,046 control chromosomes in the GnomAD database, including 15,120 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 0.44 (15120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 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: 0.444 AC: 67511 AN: 151928 Hom.: 15111 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.444 AC: 67543 AN: 152046 Hom.: 15120 Cov.: 32 AF XY: 0.444 AC XY: 32991 AN XY: 74334

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.458

Alfa AF: 0.460 Hom.: 22569

Bravo AF: 0.439

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2182880; hg19: chr13-27370669;