rs12605520
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032649.6(CNDP1):c.154-54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,596,032 control chromosomes in the GnomAD database, including 98,464 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 0.30 ( 7693 hom., cov: 32)
Exomes 𝑓: 0.35 ( 90771 hom. )
Consequence
CNDP1
NM_032649.6 intron
NM_032649.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.661
Genes affected
CNDP1 (HGNC:20675): (carnosine dipeptidase 1) This gene encodes a member of the M20 metalloprotease family. The encoded protein is specifically expressed in the brain, is a homodimeric dipeptidase which was identified as human carnosinase. This gene contains trinucleotide (CTG) repeat length polymorphism in the coding region. [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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNDP1 | NM_032649.6 | c.154-54C>T | intron_variant | ENST00000358821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNDP1 | ENST00000358821.8 | c.154-54C>T | intron_variant | 1 | NM_032649.6 | P1 | |||
CNDP1 | ENST00000582365.1 | c.25-54C>T | intron_variant | 5 | |||||
CNDP1 | ENST00000585136.1 | n.319-54C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.302 AC: 45912AN: 152018Hom.: 7691 Cov.: 32
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GnomAD4 exome AF: 0.351 AC: 506640AN: 1443896Hom.: 90771 AF XY: 0.353 AC XY: 254264AN XY: 719354
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GnomAD4 genome ? AF: 0.302 AC: 45933AN: 152136Hom.: 7693 Cov.: 32 AF XY: 0.306 AC XY: 22727AN XY: 74346
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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