13-85793850-C-CT

Position:

• chr13-85793850-C-CT

Variant summary

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

The NM_032229.3(SLITRK6):​c.*132dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0381 in 1,019,602 control chromosomes in the GnomAD database, including 731 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.039 (175 hom., cov: 31)
  • Exomes 𝑓: 0.038 (556 hom.)
• Consequence: SLITRK6 NM_032229.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.93

Genes affected

SLITRK6 (HGNC:23503): (SLIT and NTRK like family member 6) 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. This protein functions as a regulator of neurite outgrowth required for normal hearing and vision. Mutations in this gene are a cause of myopia and deafness. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-85793850-C-CT is Benign according to our data. Variant chr13-85793850-C-CT is described in ClinVar as [Benign]. Clinvar id is 1277975.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK6	NM_032229.3	c.*132dupA		3_prime_UTR_variant	2/2	ENST00000647374.2	NP_115605.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLITRK6	ENST00000647374	c.*132dupA		3_prime_UTR_variant	2/2		NM_032229.3	ENSP00000495507.1
SLITRK6	ENST00000643778.1	c.*132dupA		downstream_gene_variant				ENSP00000496428.1

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5885 AN: 150928 Hom.: 174 Cov.: 31

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0592

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0405

GnomAD4 exome AF: 0.0380 AC: 32967 AN: 868562 Hom.: 556 Cov.: 12 AF XY: 0.0396 AC XY: 16985 AN XY: 429348

Gnomad4 AFR exome AF: 0.0201

Gnomad4 AMR exome AF: 0.0225

Gnomad4 ASJ exome AF: 0.0567

Gnomad4 EAS exome AF: 0.0521

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0823

Gnomad4 NFE exome AF: 0.0314

Gnomad4 OTH exome AF: 0.0414

GnomAD4 genome AF: 0.0391 AC: 5906 AN: 151040 Hom.: 175 Cov.: 31 AF XY: 0.0437 AC XY: 3219 AN XY: 73730

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0592

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.0345

Gnomad4 OTH AF: 0.0430

Bravo AF: 0.0322

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2019

- -

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: rs556378713; hg19: chr13-86367985;