chr11-68760217-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001876.4(CPT1A):c.2142+8C>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 0.000000692 in 1,444,422 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001876.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.2142+8C>A | splice_region_variant, intron_variant | ENST00000265641.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.2142+8C>A | splice_region_variant, intron_variant | 1 | NM_001876.4 | P1 | |||
CPT1A | ENST00000376618.6 | c.2142+8C>A | splice_region_variant, intron_variant | 1 | |||||
CPT1A | ENST00000540367.5 | c.2142+8C>A | splice_region_variant, intron_variant | 1 | |||||
CPT1A | ENST00000539743.5 | c.2142+8C>A | splice_region_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1444422Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 717738
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 05, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.