13-83882600-T-C

Variant names:

• chr13-83882600-T-C
• rs9546538
• ENST00000654693.1:n.145T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654693.1(ENSG00000285680):​n.145T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,032 control chromosomes in the GnomAD database, including 6,146 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 0.28 (6146 hom., cov: 32)
• Consequence: ENSG00000285680 ENST00000654693.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 13 publications found

Genes affected

ENSG00000285680 (HGNC:):

SLITRK1 (HGNC:20297): (SLIT and NTRK like family member 1) This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. However, the protein encoded by this gene lacks the region of homology to neurotrophin receptors. This protein is thought to be involved in neurite outgrowth. Mutations in this gene may be associated with Tourette syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

SLITRK1 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown, AD Classification: LIMITED, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
• trichotillomania

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654693.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLITRK1	NM_001281503.2	MANE Select	c.-650A>G		upstream_gene	N/A	NP_001268432.1	Q96PX8
	SLITRK1	NM_052910.2		c.-1093A>G		upstream_gene	N/A	NP_443142.1	Q96PX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285680	ENST00000654693.1		n.145T>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000285680	ENST00000649183.1		n.202-3682T>C		intron	N/A
	ENSG00000285680	ENST00000667130.2		n.224+3790T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42563 AN: 151914 Hom.: 6136 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.280 AC: 42604 AN: 152032 Hom.: 6146 Cov.: 32 AF XY: 0.279 AC XY: 20760 AN XY: 74308

African (AFR) AF: 0.288 AC: 11930 AN: 41466

American (AMR) AF: 0.319 AC: 4879 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2018 AN: 5154

South Asian (SAS) AF: 0.389 AC: 1868 AN: 4804

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10590

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17937 AN: 67954

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.272 Hom.: 9700

Bravo AF: 0.289

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		-0.027
PromoterAI		0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9546538; hg19: chr13-84456735;