13-83878257-C-T

Position:

• chr13-83878257-C-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_001281503.2(SLITRK1):​c.*1160G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 152,532 control chromosomes in the GnomAD database, including 483 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.054 (483 hom., cov: 31)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: SLITRK1 NM_001281503.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.63

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 -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 13-83878257-C-T is Benign according to our data. Variant chr13-83878257-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 312482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK1	NM_001281503.2	c.*1160G>A		3_prime_UTR_variant	2/2	ENST00000674365.1	NP_001268432.1
SLITRK1	NM_052910.2	c.*1160G>A		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.*1160G>A		3_prime_UTR_variant	2/2		NM_001281503.2	ENSP00000501349.1
SLITRK1	ENST00000377084	c.*1160G>A		3_prime_UTR_variant	1/1			ENSP00000366288.2
ENSG00000285680	ENST00000649183.1	n.93+274C>T		intron_variant
ENSG00000285680	ENST00000667130.1	n.96+274C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0544 AC: 8269 AN: 151992 Hom.: 482 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0536

GnomAD4 exome AF: 0.0118 AC: 5 AN: 422 Hom.: 0 Cov.: 0 AF XY: 0.0157 AC XY: 4 AN XY: 254

Gnomad4 FIN exome AF: 0.0120

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0544 AC: 8282 AN: 152110 Hom.: 483 Cov.: 31 AF XY: 0.0534 AC XY: 3968 AN XY: 74358

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0293

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00643

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0283 Hom.: 42

Bravo AF: 0.0582

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

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	-0.34
CADD	Benign	18
DANN	Benign	0.95

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: rs9602286; hg19: chr13-84452392;