13-105453241-C-T

Position:

• chr13-105453241-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 0.511 in 151,978 control chromosomes in the GnomAD database, including 20,082 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 0.51 (20082 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

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 (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105453241C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77569 AN: 151860 Hom.: 20077 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.511 AC: 77614 AN: 151978 Hom.: 20082 Cov.: 32 AF XY: 0.508 AC XY: 37702 AN XY: 74282

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.530

Alfa AF: 0.521 Hom.: 3429

Bravo AF: 0.509

Asia WGS AF: 0.435 AC: 1515 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	2.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9519671; hg19: chr13-106105590;