2-124903032-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001367498.1(CNTNAP5):c.3587C>A(p.Thr1196Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,455,496 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. 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. T1196M) has been classified as Benign.
Frequency
Consequence
NM_001367498.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTNAP5 | NM_001367498.1 | c.3587C>A | p.Thr1196Lys | missense_variant | 22/24 | ENST00000682447.1 | |
CNTNAP5 | NM_130773.4 | c.3584C>A | p.Thr1195Lys | missense_variant | 22/24 | ||
CNTNAP5 | XM_017003316.2 | c.3347C>A | p.Thr1116Lys | missense_variant | 21/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTNAP5 | ENST00000682447.1 | c.3587C>A | p.Thr1196Lys | missense_variant | 22/24 | NM_001367498.1 | A1 | ||
CNTNAP5 | ENST00000431078.1 | c.3584C>A | p.Thr1195Lys | missense_variant | 22/24 | 1 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000168 AC: 4AN: 237804Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128688
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1455496Hom.: 0 Cov.: 31 AF XY: 0.00000415 AC XY: 3AN XY: 723428
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at