13-85793742-T-C

Position:

• chr13-85793742-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032229.3(SLITRK6):​c.*241A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 399,448 control chromosomes in the GnomAD database, including 111,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.76 (44734 hom., cov: 32)
  • Exomes 𝑓: 0.73 (67121 hom.)
• Consequence: SLITRK6 NM_032229.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.368

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 13-85793742-T-C is Benign according to our data. Variant chr13-85793742-T-C is described in ClinVar as [Benign]. Clinvar id is 1257873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLITRK6	NM_032229.3	c.*241A>G		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.*241A>G		3_prime_UTR_variant	2/2		NM_032229.3	ENSP00000495507.1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115843 AN: 151672 Hom.: 44676 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.732 AC: 181242 AN: 247658 Hom.: 67121 Cov.: 4 AF XY: 0.730 AC XY: 92521 AN XY: 126782

Gnomad4 AFR exome AF: 0.862

Gnomad4 AMR exome AF: 0.636

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.663

Gnomad4 SAS exome AF: 0.712

Gnomad4 FIN exome AF: 0.832

Gnomad4 NFE exome AF: 0.741

Gnomad4 OTH exome AF: 0.726

GnomAD4 genome AF: 0.764 AC: 115966 AN: 151790 Hom.: 44734 Cov.: 32 AF XY: 0.765 AC XY: 56798 AN XY: 74200

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.731

Alfa AF: 0.712 Hom.: 3000

Bravo AF: 0.753

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.83

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: rs1337266; hg19: chr13-86367877; COSMIC: COSV68390030; COSMIC: COSV68390030;