13-85795268-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032229.3(SLITRK6):āc.1241A>Gā(p.Gln414Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0182 in 1,612,632 control chromosomes in the GnomAD database, including 3,418 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032229.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLITRK6 | NM_032229.3 | c.1241A>G | p.Gln414Arg | missense_variant | 2/2 | ENST00000647374.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLITRK6 | ENST00000647374.2 | c.1241A>G | p.Gln414Arg | missense_variant | 2/2 | NM_032229.3 | P1 | ||
SLITRK6 | ENST00000643778.1 | c.1241A>G | p.Gln414Arg | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0837 AC: 12707AN: 151818Hom.: 1701 Cov.: 32
GnomAD3 exomes AF: 0.0264 AC: 6548AN: 248254Hom.: 717 AF XY: 0.0228 AC XY: 3074AN XY: 134732
GnomAD4 exome AF: 0.0113 AC: 16567AN: 1460696Hom.: 1718 Cov.: 35 AF XY: 0.0114 AC XY: 8318AN XY: 726616
GnomAD4 genome AF: 0.0837 AC: 12716AN: 151936Hom.: 1700 Cov.: 32 AF XY: 0.0828 AC XY: 6152AN XY: 74286
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Gln414Arg in exon 2 of SLITRK6: This variant is not expected to have clinical significance because it has been identified in 29.28% (2864/9782) of African chr omosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.o rg; dbSNP rs17080147). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2017 | 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
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at