chr7-147132472-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_014141.6(CNTNAP2):c.1311C>T(p.Ile437Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00346 in 1,613,648 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014141.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CNTNAP2 | NM_014141.6 | c.1311C>T | p.Ile437Ile | synonymous_variant | Exon 8 of 24 | ENST00000361727.8 | NP_054860.1 | |
CNTNAP2 | XM_017011950.3 | c.1311C>T | p.Ile437Ile | synonymous_variant | Exon 8 of 14 | XP_016867439.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00333 AC: 507AN: 152120Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00343 AC: 862AN: 251146Hom.: 3 AF XY: 0.00364 AC XY: 494AN XY: 135726
GnomAD4 exome AF: 0.00348 AC: 5082AN: 1461410Hom.: 12 Cov.: 32 AF XY: 0.00370 AC XY: 2688AN XY: 727010
GnomAD4 genome AF: 0.00332 AC: 506AN: 152238Hom.: 4 Cov.: 32 AF XY: 0.00330 AC XY: 246AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:4
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CNTNAP2: BP4, BP7 -
not specified Benign:3
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Cortical dysplasia-focal epilepsy syndrome Uncertain:1Benign:1
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Pitt-Hopkins-like syndrome Uncertain:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
CNTNAP2-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