chr13-109919863-C-T

Position:

• chr13-109919863-C-T

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 0.632 in 151,976 control chromosomes in the GnomAD database, including 30,504 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 0.63 (30504 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109919863C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95992 AN: 151858 Hom.: 30487 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.632 AC: 96048 AN: 151976 Hom.: 30504 Cov.: 31 AF XY: 0.625 AC XY: 46476 AN XY: 74308

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.640

Alfa AF: 0.656 Hom.: 14433

Bravo AF: 0.636

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7323507; hg19: chr13-110572210;