2-124417444-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001367498.1(CNTNAP5):c.383C>A(p.Thr128Asn) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367498.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTNAP5 | NM_001367498.1 | c.383C>A | p.Thr128Asn | missense_variant, splice_region_variant | 4/24 | ENST00000682447.1 | NP_001354427.1 | |
CNTNAP5 | NM_130773.4 | c.383C>A | p.Thr128Asn | missense_variant, splice_region_variant | 4/24 | NP_570129.1 | ||
CNTNAP5 | XM_017003316.2 | c.383C>A | p.Thr128Asn | missense_variant, splice_region_variant | 4/23 | XP_016858805.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP5 | ENST00000682447.1 | c.383C>A | p.Thr128Asn | missense_variant, splice_region_variant | 4/24 | NM_001367498.1 | ENSP00000508115.1 | |||
CNTNAP5 | ENST00000431078.1 | c.383C>A | p.Thr128Asn | missense_variant, splice_region_variant | 4/24 | 1 | ENSP00000399013.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248928Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135028
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461442Hom.: 1 Cov.: 30 AF XY: 0.0000440 AC XY: 32AN XY: 726986
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 23, 2024 | The c.383C>A (p.T128N) alteration is located in exon 4 (coding exon 4) of the CNTNAP5 gene. This alteration results from a C to A substitution at nucleotide position 383, causing the threonine (T) at amino acid position 128 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at