chr9-39078834-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_033655.5(CNTNAP3):c.3529G>C(p.Ala1177Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP3 | ENST00000297668.11 | c.3529G>C | p.Ala1177Pro | missense_variant | Exon 22 of 24 | 1 | NM_033655.5 | ENSP00000297668.6 | ||
CNTNAP3 | ENST00000377656.6 | c.3286G>C | p.Ala1096Pro | missense_variant | Exon 21 of 23 | 1 | ENSP00000366884.2 | |||
CNTNAP3 | ENST00000477002.1 | n.275G>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 | |||||
CNTNAP3 | ENST00000493965.5 | n.274-378G>C | intron_variant | Intron 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 47
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000290 AC: 4AN: 1380900Hom.: 0 Cov.: 175 AF XY: 0.00000293 AC XY: 2AN XY: 681466
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 47 AF XY: 0.00 AC XY: 0AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3529G>C (p.A1177P) alteration is located in exon 22 (coding exon 22) of the CNTNAP3 gene. This alteration results from a G to C substitution at nucleotide position 3529, causing the alanine (A) at amino acid position 1177 to be replaced by a proline (P). 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