13-105182819-C-T

Position:

• chr13-105182819-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.0266 in 151,192 control chromosomes in the GnomAD database, including 96 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 0.027 (96 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0778 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: 0.0267 AC: 4029 AN: 151080 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00602

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0266 AC: 4024 AN: 151192 Hom.: 96 Cov.: 32 AF XY: 0.0282 AC XY: 2085 AN XY: 73842

Gnomad4 AFR AF: 0.00600

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0239 Hom.: 24

Bravo AF: 0.0313

Asia WGS AF: 0.0270 AC: 92 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	23
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16966085; hg19: chr13-105835170;