7-120989752-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024913.5(CPED1):c.131C>G(p.Ala44Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024913.5 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 |
---|---|---|---|---|---|---|---|
CPED1 | NM_024913.5 | c.131C>G | p.Ala44Gly | missense_variant | 2/23 | ENST00000310396.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPED1 | ENST00000310396.10 | c.131C>G | p.Ala44Gly | missense_variant | 2/23 | 1 | NM_024913.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 151974Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251494Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135922
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727248
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.131C>G (p.A44G) alteration is located in exon 2 (coding exon 1) of the CPED1 gene. This alteration results from a C to G substitution at nucleotide position 131, causing the alanine (A) at amino acid position 44 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