2-124903032-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001367498.1(CNTNAP5):c.3587C>T(p.Thr1196Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 1,607,612 control chromosomes in the GnomAD database, including 393 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001367498.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTNAP5 | NM_001367498.1 | c.3587C>T | p.Thr1196Met | missense_variant | Exon 22 of 24 | ENST00000682447.1 | NP_001354427.1 | |
CNTNAP5 | NM_130773.4 | c.3584C>T | p.Thr1195Met | missense_variant | Exon 22 of 24 | NP_570129.1 | ||
CNTNAP5 | XM_017003316.2 | c.3347C>T | p.Thr1116Met | missense_variant | Exon 21 of 23 | XP_016858805.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP5 | ENST00000682447.1 | c.3587C>T | p.Thr1196Met | missense_variant | Exon 22 of 24 | NM_001367498.1 | ENSP00000508115.1 | |||
CNTNAP5 | ENST00000431078.1 | c.3584C>T | p.Thr1195Met | missense_variant | Exon 22 of 24 | 1 | ENSP00000399013.1 |
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 2285AN: 152098Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.0154 AC: 3661AN: 237804Hom.: 40 AF XY: 0.0165 AC XY: 2122AN XY: 128688
GnomAD4 exome AF: 0.0208 AC: 30229AN: 1455396Hom.: 361 Cov.: 31 AF XY: 0.0210 AC XY: 15164AN XY: 723376
GnomAD4 genome AF: 0.0150 AC: 2287AN: 152216Hom.: 32 Cov.: 32 AF XY: 0.0135 AC XY: 1003AN XY: 74422
ClinVar
Submissions by phenotype
CNTNAP5-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at