chr13-105182819-C-T

Variant names:

• chr13-105182819-C-T
• rs16966085

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;