9-128420930-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016174.5(CERCAM):c.53C>T(p.Pro18Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,439,018 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 Likely benign (★).
Frequency
Consequence
NM_016174.5 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERCAM | NM_016174.5 | c.53C>T | p.Pro18Leu | missense_variant | Exon 1 of 13 | ENST00000372838.9 | NP_057258.3 | |
CERCAM | XM_047423450.1 | c.-490C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 14 | XP_047279406.1 | |||
CERCAM | XM_047423450.1 | c.-490C>T | 5_prime_UTR_variant | Exon 1 of 14 | XP_047279406.1 | |||
CERCAM | NM_001286760.1 | c.-38+1652C>T | intron_variant | Intron 1 of 12 | NP_001273689.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152092Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000295 AC: 2AN: 67708Hom.: 0 AF XY: 0.0000252 AC XY: 1AN XY: 39754
GnomAD4 exome AF: 0.0000101 AC: 13AN: 1286926Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 7AN XY: 633940
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152092Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at