chr13-85796470-A-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032229.3(SLITRK6):c.39T>A(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,575,392 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032229.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLITRK6 | ENST00000647374.2 | c.39T>A | p.Leu13Leu | synonymous_variant | Exon 2 of 2 | NM_032229.3 | ENSP00000495507.1 | |||
SLITRK6 | ENST00000643778.1 | c.39T>A | p.Leu13Leu | synonymous_variant | Exon 3 of 3 | ENSP00000496428.1 | ||||
SLITRK6 | ENST00000645642.1 | n.521-527T>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.00802 AC: 1218AN: 151860Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.00214 AC: 453AN: 211436Hom.: 5 AF XY: 0.00157 AC XY: 180AN XY: 114904
GnomAD4 exome AF: 0.000688 AC: 980AN: 1423414Hom.: 13 Cov.: 34 AF XY: 0.000570 AC XY: 403AN XY: 706748
GnomAD4 genome AF: 0.00801 AC: 1217AN: 151978Hom.: 23 Cov.: 32 AF XY: 0.00775 AC XY: 576AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:2
p.Leu13Leu in exon 2 of SLITRK6: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 2.83% (264/9342) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs74104527). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at