chr22-50570914-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152246.3(CPT1B):c.2005G>A(p.Val669Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V669L) has been classified as Uncertain significance.
Frequency
Consequence
NM_152246.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT1B | NM_152246.3 | c.2005G>A | p.Val669Ile | missense_variant | Exon 16 of 20 | ENST00000312108.12 | NP_689452.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPT1B | ENST00000312108.12 | c.2005G>A | p.Val669Ile | missense_variant | Exon 16 of 20 | 1 | NM_152246.3 | ENSP00000312189.8 | ||
CHKB-CPT1B | ENST00000453634.5 | n.*2230G>A | non_coding_transcript_exon_variant | Exon 19 of 23 | 5 | ENSP00000457031.1 | ||||
CHKB-CPT1B | ENST00000453634.5 | n.*2230G>A | 3_prime_UTR_variant | Exon 19 of 23 | 5 | ENSP00000457031.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249194Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134952
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461384Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726992
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2005G>A (p.V669I) alteration is located in exon 16 (coding exon 15) of the CPT1B gene. This alteration results from a G to A substitution at nucleotide position 2005, causing the valine (V) at amino acid position 669 to be replaced by an isoleucine (I). 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