13-85793838-CT-C

Position:

• chr13-85793838-CT-C

Variant summary

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

The NM_032229.3(SLITRK6):​c.*144delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 938,462 control chromosomes in the GnomAD database, including 43,415 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (5889 hom., cov: 23)
  • Exomes 𝑓: 0.30 (37526 hom.)
• Consequence: SLITRK6 NM_032229.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0960

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 13-85793838-CT-C is Benign according to our data. Variant chr13-85793838-CT-C is described in ClinVar as [Benign]. Clinvar id is 1263017.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK6	NM_032229.3	c.*144delA		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.*144delA		3_prime_UTR_variant	2/2		NM_032229.3	ENSP00000495507.1
SLITRK6	ENST00000643778.1	c.*144delA		downstream_gene_variant				ENSP00000496428.1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37739 AN: 151148 Hom.: 5879 Cov.: 23

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.297 AC: 233420 AN: 787198 Hom.: 37526 Cov.: 3 AF XY: 0.298 AC XY: 116758 AN XY: 392356

Gnomad4 AFR exome AF: 0.0747

Gnomad4 AMR exome AF: 0.357

Gnomad4 ASJ exome AF: 0.288

Gnomad4 EAS exome AF: 0.605

Gnomad4 SAS exome AF: 0.312

Gnomad4 FIN exome AF: 0.227

Gnomad4 NFE exome AF: 0.289

Gnomad4 OTH exome AF: 0.302

GnomAD4 genome AF: 0.250 AC: 37766 AN: 151264 Hom.: 5889 Cov.: 23 AF XY: 0.251 AC XY: 18565 AN XY: 73834

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.289

Alfa AF: 0.259 Hom.: 699

Bravo AF: 0.253

Asia WGS AF: 0.458 AC: 1593 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

Nov 12, 2018

- -

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: rs34633805; hg19: chr13-86367973;