13-105815706-C-T

Variant names:

• chr13-105815706-C-T
• rs1328089

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 0.669 in 152,024 control chromosomes in the GnomAD database, including 35,166 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 0.67 (35166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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: 0.670 AC: 101727 AN: 151906 Hom.: 35175 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.669 AC: 101743 AN: 152024 Hom.: 35166 Cov.: 32 AF XY: 0.670 AC XY: 49772 AN XY: 74288

African (AFR) AF: 0.514 AC: 21273 AN: 41418

American (AMR) AF: 0.589 AC: 8992 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2269 AN: 3470

East Asian (EAS) AF: 0.815 AC: 4220 AN: 5176

South Asian (SAS) AF: 0.531 AC: 2561 AN: 4826

European-Finnish (FIN) AF: 0.808 AC: 8540 AN: 10564

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51492 AN: 67986

Other (OTH) AF: 0.665 AC: 1405 AN: 2112

Alfa AF: 0.712 Hom.: 107148

Bravo AF: 0.650

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.41
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1328089; hg19: chr13-106468055;