13-83878283-A-G

Position:

• chr13-83878283-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000285680 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id is 312484.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-83878283-A-G is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK1	NM_001281503.2	c.*1134T>C		3_prime_UTR_variant	2/2	ENST00000674365.1	NP_001268432.1
SLITRK1	NM_052910.2	c.*1134T>C		3_prime_UTR_variant	1/1		NP_443142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLITRK1	ENST00000674365	c.*1134T>C		3_prime_UTR_variant	2/2		NM_001281503.2	ENSP00000501349.1
SLITRK1	ENST00000377084	c.*1134T>C		3_prime_UTR_variant	1/1			ENSP00000366288.2
ENSG00000285680	ENST00000649183.1	n.93+300A>G		intron_variant
ENSG00000285680	ENST00000667130.1	n.96+300A>G		intron_variant

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

Gnomad4 FIN exome AF: 0.0164

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.00621

Gnomad4 AMR AF: 0.0733

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.00762

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0348 Hom.: 115

Bravo AF: 0.0313

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Tourette syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.89

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

Publications

LitVar

Other links and lift over

dbSNP: rs3737193; hg19: chr13-84452418;