rs201870376
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001199753.2(CPT1C):c.1731+7T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00635 in 1,614,164 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001199753.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1C | NM_001199753.2 | c.1731+7T>A | splice_region_variant, intron_variant | ENST00000598293.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1C | ENST00000598293.6 | c.1731+7T>A | splice_region_variant, intron_variant | 2 | NM_001199753.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00430 AC: 654AN: 152210Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00367 AC: 923AN: 251180Hom.: 5 AF XY: 0.00364 AC XY: 495AN XY: 135846
GnomAD4 exome AF: 0.00656 AC: 9595AN: 1461836Hom.: 33 Cov.: 31 AF XY: 0.00644 AC XY: 4681AN XY: 727214
GnomAD4 genome ? AF: 0.00429 AC: 654AN: 152328Hom.: 2 Cov.: 32 AF XY: 0.00384 AC XY: 286AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CPT1C: BP4, BS2 - |
Hereditary spastic paraplegia 73 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at