rs10189889
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001367498.1(CNTNAP5):c.2077+39929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0231 in 152,054 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.023 ( 46 hom., cov: 32)
Consequence
CNTNAP5
NM_001367498.1 intron
NM_001367498.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.534
Genes affected
CNTNAP5 (HGNC:18748): (contactin associated protein family member 5) This gene product belongs to the neurexin family, members of which function in the vertebrate nervous system as cell adhesion molecules and receptors. This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, and thrombospondin N-terminal-like domains. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0231 (3505/152054) while in subpopulation NFE AF= 0.0318 (2163/67992). AF 95% confidence interval is 0.0307. There are 46 homozygotes in gnomad4. There are 1593 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 46 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTNAP5 | NM_001367498.1 | c.2077+39929G>A | intron_variant | ENST00000682447.1 | |||
CNTNAP5 | NM_130773.4 | c.2074+39929G>A | intron_variant | ||||
CNTNAP5 | XM_017003316.2 | c.2077+39929G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTNAP5 | ENST00000682447.1 | c.2077+39929G>A | intron_variant | NM_001367498.1 | A1 | ||||
CNTNAP5 | ENST00000431078.1 | c.2074+39929G>A | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0231 AC: 3504AN: 151940Hom.: 46 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0231 AC: 3505AN: 152054Hom.: 46 Cov.: 32 AF XY: 0.0214 AC XY: 1593AN XY: 74348
GnomAD4 genome
?
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at