13-83233870-C-T

Position:

• chr13-83233870-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 0.288 in 151,336 control chromosomes in the GnomAD database, including 7,461 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 0.29 (7461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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: 0.288 AC: 43531 AN: 151222 Hom.: 7466 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.409

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.288 AC: 43525 AN: 151336 Hom.: 7461 Cov.: 32 AF XY: 0.296 AC XY: 21861 AN XY: 73910

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.313

Alfa AF: 0.306 Hom.: 949

Bravo AF: 0.281

Asia WGS AF: 0.304 AC: 1037 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1849391; hg19: chr13-83808005;