rs431057

chr13-85798128-A-Cchr13-85798128-A-Gchr13-85798128-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032229.3(SLITRK6):c.-25+786T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,584 control chromosomes in the GnomAD database, including 29,740 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29740 hom., cov: 31)
• Consequence: SLITRK6 NM_032229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLITRK6	NM_032229.3	c.-25+786T>G		intron_variant		ENST00000647374.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLITRK6	ENST00000647374.2	c.-25+786T>G		intron_variant			NM_032229.3	P1
SLITRK6	ENST00000643778.1	c.-25+786T>G		intron_variant				P1
SLITRK6	ENST00000645642.1	n.520+786T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94606 AN: 151466 Hom.: 29700 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.625 AC: 94711 AN: 151584 Hom.: 29740 Cov.: 31 AF XY: 0.631 AC XY: 46730 AN XY: 74098

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.645

Alfa AF: 0.611 Hom.: 36096

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.2
Dann	Benign	0.65

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: rs431057; hg19: chr13-86372263;