13-105936792-C-T

Variant names:

• chr13-105936792-C-T
• rs7336109

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 0.365 in 151,980 control chromosomes in the GnomAD database, including 11,542 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 0.37 (11542 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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: 0.365 AC: 55426 AN: 151860 Hom.: 11519 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.365 AC: 55499 AN: 151980 Hom.: 11542 Cov.: 33 AF XY: 0.363 AC XY: 26989 AN XY: 74302

African (AFR) AF: 0.580 AC: 24044 AN: 41428

American (AMR) AF: 0.248 AC: 3795 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3466

East Asian (EAS) AF: 0.148 AC: 764 AN: 5168

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4822

European-Finnish (FIN) AF: 0.368 AC: 3880 AN: 10550

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19676 AN: 67958

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.321 Hom.: 12128

Bravo AF: 0.363

Asia WGS AF: 0.265 AC: 919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.36
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7336109; hg19: chr13-106589141;