chr13-27778421-C-T

Variant names:

• chr13-27778421-C-T
• rs1326383

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 0.408 in 151,990 control chromosomes in the GnomAD database, including 12,819 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 0.41 (12819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.408 AC: 61959 AN: 151872 Hom.: 12793 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.408 AC: 62033 AN: 151990 Hom.: 12819 Cov.: 32 AF XY: 0.408 AC XY: 30318 AN XY: 74254

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.395

Alfa AF: 0.424 Hom.: 22747

Bravo AF: 0.400

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1326383; hg19: chr13-28352558;