16-76479473-T-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_033401.5(CNTNAP4):c.1817T>A(p.Phe606Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,611,040 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 Likely benign (★).
Frequency
Consequence
NM_033401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTNAP4 | ENST00000611870.5 | c.1817T>A | p.Phe606Tyr | missense_variant | Exon 12 of 24 | 1 | NM_033401.5 | ENSP00000479811.1 | ||
ENSG00000287694 | ENST00000655556.1 | n.1817T>A | non_coding_transcript_exon_variant | Exon 12 of 25 | ENSP00000499374.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458946Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 725694
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
CNTNAP4-related disorder Benign:1
This variant is classified as likely 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