chr2-124446912-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001367498.1(CNTNAP5):c.893C>T(p.Thr298Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,588 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367498.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTNAP5 | NM_001367498.1 | c.893C>T | p.Thr298Met | missense_variant | 6/24 | ENST00000682447.1 | |
CNTNAP5 | NM_130773.4 | c.893C>T | p.Thr298Met | missense_variant | 6/24 | ||
CNTNAP5 | XM_017003316.2 | c.893C>T | p.Thr298Met | missense_variant | 6/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTNAP5 | ENST00000682447.1 | c.893C>T | p.Thr298Met | missense_variant | 6/24 | NM_001367498.1 | A1 | ||
CNTNAP5 | ENST00000431078.1 | c.893C>T | p.Thr298Met | missense_variant | 6/24 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248254Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134592
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461410Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726988
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.893C>T (p.T298M) alteration is located in exon 6 (coding exon 6) of the CNTNAP5 gene. This alteration results from a C to T substitution at nucleotide position 893, causing the threonine (T) at amino acid position 298 to be replaced by a methionine (M). 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