chr13-83877373-TA-T

Position:

• chr13-83877373-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001281503.2(SLITRK1):​c.*2043delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (19515 hom., cov: 0)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLITRK1 NM_001281503.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.680

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-83877373-TA-T is Benign according to our data. Variant chr13-83877373-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 312476.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK1	NM_001281503.2	c.*2043delT		3_prime_UTR_variant	2/2	ENST00000674365.1	NP_001268432.1
SLITRK1	NM_052910.2	c.*2043delT		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.*2043delT		3_prime_UTR_variant	2/2		NM_001281503.2	ENSP00000501349.1
SLITRK1	ENST00000377084	c.*2043delT		3_prime_UTR_variant	1/1			ENSP00000366288.2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67189 AN: 151510 Hom.: 19451 Cov.: 0

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.422

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.444 AC: 67308 AN: 151628 Hom.: 19515 Cov.: 0 AF XY: 0.439 AC XY: 32520 AN XY: 74096

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.424

Bravo AF: 0.475

Asia WGS AF: 0.493 AC: 1714 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

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: rs66938370; hg19: chr13-84451508;