13-105451011-C-T

Variant names:

• chr13-105451011-C-T
• rs3916965

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.322 in 152,036 control chromosomes in the GnomAD database, including 9,378 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 0.32 (9378 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 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: 0.322 AC: 48967 AN: 151920 Hom.: 9378 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.322 AC: 48972 AN: 152036 Hom.: 9378 Cov.: 33 AF XY: 0.330 AC XY: 24547 AN XY: 74338

African (AFR) AF: 0.113 AC: 4685 AN: 41484

American (AMR) AF: 0.389 AC: 5936 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.634 AC: 3276 AN: 5170

South Asian (SAS) AF: 0.431 AC: 2081 AN: 4828

European-Finnish (FIN) AF: 0.438 AC: 4625 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25983 AN: 67954

Other (OTH) AF: 0.324 AC: 686 AN: 2116

Alfa AF: 0.295 Hom.: 3685

Bravo AF: 0.308

Asia WGS AF: 0.465 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.22
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3916965; hg19: chr13-106103360;