13-109545812-C-T

Position:

• chr13-109545812-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650264.1(ENSG00000285534):​n.933+14589G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,256 control chromosomes in the GnomAD database, including 559 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 0.058 (559 hom., cov: 33)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650264.1	n.933+14589G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8818 AN: 152138 Hom.: 561 Cov.: 33

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0579 AC: 8809 AN: 152256 Hom.: 559 Cov.: 33 AF XY: 0.0631 AC XY: 4694 AN XY: 74436

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0503 Hom.: 57

Bravo AF: 0.0616

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410425; hg19: chr13-110198159;