22-50571473-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152246.3(CPT1B):c.1642T>G(p.Cys548Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152246.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1B | NM_152246.3 | c.1642T>G | p.Cys548Gly | missense_variant | 14/20 | ENST00000312108.12 | |
CHKB-CPT1B | NR_027928.2 | n.3212T>G | non_coding_transcript_exon_variant | 24/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1B | ENST00000312108.12 | c.1642T>G | p.Cys548Gly | missense_variant | 14/20 | 1 | NM_152246.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 248898Hom.: 1 AF XY: 0.0000594 AC XY: 8AN XY: 134766
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461442Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727010
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.1642T>G (p.C548G) alteration is located in exon 14 (coding exon 13) of the CPT1B gene. This alteration results from a T to G substitution at nucleotide position 1642, causing the cysteine (C) at amino acid position 548 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at