chr18-74571177-ACT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_032649.6(CNDP1):c.757-6_757-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,586,890 control chromosomes in the GnomAD database, including 133 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0039 ( 12 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 121 hom. )
Consequence
CNDP1
NM_032649.6 splice_region, splice_polypyrimidine_tract, intron
NM_032649.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.806
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 -10 ACMG points.
BP6
?
Variant 18-74571177-ACT-A is Benign according to our data. Variant chr18-74571177-ACT-A is described in ClinVar as [Benign]. Clinvar id is 770278.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.067 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNDP1 | NM_032649.6 | c.757-6_757-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000358821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNDP1 | ENST00000358821.8 | c.757-6_757-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032649.6 | P1 | |||
CNDP1 | ENST00000582365.1 | c.628-6_628-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
CNDP1 | ENST00000584316.5 | c.*225-6_*225-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 4 | |||||
CNDP1 | ENST00000584004.5 | n.281-6_281-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00389 AC: 592AN: 152066Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.0114 AC: 2850AN: 251080Hom.: 109 AF XY: 0.00871 AC XY: 1182AN XY: 135692
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GnomAD4 exome AF: 0.00252 AC: 3614AN: 1434706Hom.: 121 AF XY: 0.00221 AC XY: 1579AN XY: 715472
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GnomAD4 genome ? AF: 0.00389 AC: 592AN: 152184Hom.: 12 Cov.: 32 AF XY: 0.00426 AC XY: 317AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 9
Find out detailed SpliceAI scores and Pangolin per-transcript scores at