11-68761622-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001876.4(CPT1A):āc.1941C>Gā(p.Ala647Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 1,614,098 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001876.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | ENST00000265641.10 | NP_001867.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | 1 | NM_001876.4 | ENSP00000265641.4 | ||
CPT1A | ENST00000376618.6 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | 1 | ENSP00000365803.2 | |||
CPT1A | ENST00000540367.5 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 15 of 18 | 1 | ENSP00000439084.1 | |||
CPT1A | ENST00000539743.5 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 15 of 18 | 5 | ENSP00000446108.1 |
Frequencies
GnomAD3 genomes AF: 0.00818 AC: 1244AN: 152094Hom.: 15 Cov.: 31
GnomAD3 exomes AF: 0.00215 AC: 540AN: 251494Hom.: 14 AF XY: 0.00157 AC XY: 213AN XY: 135920
GnomAD4 exome AF: 0.000882 AC: 1289AN: 1461886Hom.: 26 Cov.: 32 AF XY: 0.000778 AC XY: 566AN XY: 727246
GnomAD4 genome AF: 0.00815 AC: 1241AN: 152212Hom.: 14 Cov.: 31 AF XY: 0.00796 AC XY: 592AN XY: 74414
ClinVar
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Benign:3
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not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at