13-83233870-C-T

Variant names:

• chr13-83233870-C-T
• rs1849391

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;