chr19-8302552-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_016579.4(CD320):c.760C>T(p.Arg254Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R254R) has been classified as Uncertain significance.
Frequency
Consequence
NM_016579.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD320 | NM_016579.4 | c.760C>T | p.Arg254Ter | stop_gained | 5/5 | ENST00000301458.10 | |
CD320 | NM_001165895.2 | c.634C>T | p.Arg212Ter | stop_gained | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD320 | ENST00000301458.10 | c.760C>T | p.Arg254Ter | stop_gained | 5/5 | 1 | NM_016579.4 | P1 | |
CD320 | ENST00000596002.5 | c.*1048C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 | ||||
CD320 | ENST00000537716.6 | c.634C>T | p.Arg212Ter | stop_gained | 4/4 | 2 | |||
CD320 | ENST00000599573.1 | c.*360C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250926Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135670
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461748Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727150
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74472
ClinVar
Submissions by phenotype
Methylmalonic acidemia due to transcobalamin receptor defect Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 12, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 1063339). This variant has not been reported in the literature in individuals affected with CD320-related conditions. This variant is present in population databases (rs750760449, gnomAD 0.008%). This sequence change creates a premature translational stop signal (p.Arg254*) in the CD320 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 29 amino acid(s) of the CD320 protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at