9-39078774-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033655.5(CNTNAP3):c.3589G>T(p.Val1197Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,519,774 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_033655.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP3 | ENST00000297668.11 | c.3589G>T | p.Val1197Leu | missense_variant | Exon 22 of 24 | 1 | NM_033655.5 | ENSP00000297668.6 | ||
CNTNAP3 | ENST00000377656.6 | c.3346G>T | p.Val1116Leu | missense_variant | Exon 21 of 23 | 1 | ENSP00000366884.2 | |||
CNTNAP3 | ENST00000493965.5 | n.274-318G>T | intron_variant | Intron 3 of 4 | 5 | |||||
CNTNAP3 | ENST00000477002.1 | n.*44G>T | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152114Hom.: 0 Cov.: 40
GnomAD3 exomes AF: 0.000924 AC: 23AN: 24904Hom.: 0 AF XY: 0.000899 AC XY: 12AN XY: 13344
GnomAD4 exome AF: 0.0000782 AC: 107AN: 1367546Hom.: 0 Cov.: 92 AF XY: 0.0000845 AC XY: 57AN XY: 674480
GnomAD4 genome AF: 0.000145 AC: 22AN: 152228Hom.: 0 Cov.: 40 AF XY: 0.000188 AC XY: 14AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3589G>T (p.V1197L) alteration is located in exon 22 (coding exon 22) of the CNTNAP3 gene. This alteration results from a G to T substitution at nucleotide position 3589, causing the valine (V) at amino acid position 1197 to be replaced by a leucine (L). 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