16-76427578-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_033401.5(CNTNAP4):c.517G>A(p.Glu173Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,611,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_033401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP4 | ENST00000611870.5 | c.517G>A | p.Glu173Lys | missense_variant | Exon 4 of 24 | 1 | NM_033401.5 | ENSP00000479811.1 | ||
ENSG00000287694 | ENST00000655556.1 | n.517G>A | non_coding_transcript_exon_variant | Exon 4 of 25 | ENSP00000499374.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459832Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 726192
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
CNTNAP4-related disorder Uncertain:1
The CNTNAP4 c.130G>A variant is predicted to result in the amino acid substitution p.Glu44Lys. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at