13-104531488-C-G

Position:

• chr13-104531488-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 0.375 in 151,972 control chromosomes in the GnomAD database, including 12,177 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 (12177 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104531488C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56936 AN: 151854 Hom.: 12177 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.375 AC: 56942 AN: 151972 Hom.: 12177 Cov.: 32 AF XY: 0.381 AC XY: 28304 AN XY: 74284

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.380

Alfa AF: 0.280 Hom.: 787

Bravo AF: 0.361

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7333498; hg19: chr13-105183839;