13-83878283-A-G

Variant names:

• chr13-83878283-A-G
• rs3737193
• NM_001281503.2:c.*1134T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_001281503.2(SLITRK1):​c.*1134T>C variant causes a 3 prime UTR change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 152,682 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.028 (107 hom., cov: 31)
  • Exomes 𝑓: 0.016 (0 hom.)
• Consequence: SLITRK1 NM_001281503.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 8.38
• Publications: 5 publications found

Genes affected

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)

ENSG00000285680 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant 13-83878283-A-G is Benign according to our data. Variant chr13-83878283-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 312484.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001281503.2. 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.*1134T>C		3_prime_UTR	Exon 2 of 2	NP_001268432.1	Q96PX8
	SLITRK1	NM_052910.2		c.*1134T>C		3_prime_UTR	Exon 1 of 1	NP_443142.1	Q96PX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLITRK1	ENST00000674365.1	MANE Select	c.*1134T>C		3_prime_UTR	Exon 2 of 2	ENSP00000501349.1	Q96PX8
	SLITRK1	ENST00000377084.3	TSL:6	c.*1134T>C		3_prime_UTR	Exon 1 of 1	ENSP00000366288.2	Q96PX8
	ENSG00000285680	ENST00000649183.1		n.93+300A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0275 AC: 4187 AN: 152128 Hom.: 104 Cov.: 31

Gnomad AFR AF: 0.00623

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00762

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0378

GnomAD4 exome AF: 0.0161 AC: 7 AN: 436 Hom.: 0 Cov.: 0 AF XY: 0.0152 AC XY: 4 AN XY: 264

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0164 AC: 7 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0276 AC: 4206 AN: 152246 Hom.: 107 Cov.: 31 AF XY: 0.0273 AC XY: 2035 AN XY: 74452

African (AFR) AF: 0.00621 AC: 258 AN: 41562

American (AMR) AF: 0.0733 AC: 1120 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3472

East Asian (EAS) AF: 0.0541 AC: 279 AN: 5156

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4824

European-Finnish (FIN) AF: 0.00762 AC: 81 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0313 AC: 2126 AN: 68016

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0331 Hom.: 248

Bravo AF: 0.0313

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Tourette syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.89
PhyloP100		8.4
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3737193; hg19: chr13-84452418;