13-109749199-C-G

Variant names:

• chr13-109749199-C-G
• rs9515118

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 0.68 in 151,904 control chromosomes in the GnomAD database, including 37,804 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 0.68 (37804 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 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: 0.681 AC: 103345 AN: 151782 Hom.: 37810 Cov.: 30

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.680 AC: 103354 AN: 151904 Hom.: 37804 Cov.: 30 AF XY: 0.685 AC XY: 50888 AN XY: 74250

African (AFR) AF: 0.379 AC: 15687 AN: 41352

American (AMR) AF: 0.794 AC: 12137 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3035 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3810 AN: 5148

South Asian (SAS) AF: 0.776 AC: 3739 AN: 4818

European-Finnish (FIN) AF: 0.803 AC: 8495 AN: 10580

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54014 AN: 67938

Other (OTH) AF: 0.720 AC: 1522 AN: 2114

Alfa AF: 0.729 Hom.: 4992

Bravo AF: 0.666

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs9515118; hg19: chr13-110401546;