rs16966085

Variant names:

• chr13-105182819-C-T
• rs16966085

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00600 AC: 248 AN: 41340

American (AMR) AF: 0.0816 AC: 1233 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 180 AN: 3450

East Asian (EAS) AF: 0.0283 AC: 145 AN: 5122

South Asian (SAS) AF: 0.0265 AC: 127 AN: 4796

European-Finnish (FIN) AF: 0.0292 AC: 305 AN: 10460

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1695 AN: 67626

Other (OTH) AF: 0.0350 AC: 73 AN: 2086

Alfa AF: 0.0270 Hom.: 73

Bravo AF: 0.0313

Asia WGS AF: 0.0270 AC: 92 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	23
DANN	Benign	0.68
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs16966085; hg19: chr13-105835170;