13-109749199-C-G

Position:

• chr13-109749199-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.720

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9515118; hg19: chr13-110401546;