X-143628933-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001184749.3(SLITRK4):c.2176G>A(p.Asp726Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000364 in 1,097,548 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D726E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001184749.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLITRK4 | ENST00000356928.2 | c.2176G>A | p.Asp726Asn | missense_variant | Exon 2 of 2 | 2 | NM_001184749.3 | ENSP00000349400.1 | ||
SLITRK4 | ENST00000338017.8 | c.2176G>A | p.Asp726Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000336627.4 | |||
SLITRK4 | ENST00000596188.2 | c.2176G>A | p.Asp726Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000469205.1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1097548Hom.: 0 Cov.: 30 AF XY: 0.00000827 AC XY: 3AN XY: 362928
GnomAD4 genome Cov.: 22
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.