chr19-1383928-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_SupportingPM2PP5_Moderate
The NM_024407.5(NDUFS7):āc.2T>Cā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000028 in 1,428,548 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 Pathogenic (ā ).
Frequency
Consequence
NM_024407.5 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFS7 | NM_024407.5 | c.2T>C | p.Met1? | start_lost | Exon 1 of 8 | ENST00000233627.14 | NP_077718.3 | |
NDUFS7 | NM_001363602.2 | c.2T>C | p.Met1? | start_lost | Exon 1 of 8 | NP_001350531.1 | ||
NDUFS7 | XM_017026768.3 | c.2T>C | p.Met1? | start_lost | Exon 1 of 4 | XP_016882257.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000280 AC: 4AN: 1428548Hom.: 0 Cov.: 32 AF XY: 0.00000424 AC XY: 3AN XY: 707820
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
p.Met1? (ATG>ACG): c.2 T>C in exon 1 of the NDUFS7 gene (NM_024407.4). The c.2 T>C mutation in the NDUFS7 gene alters the initiator Methionine codon and the resultant protein would be described as p.Met1?" using a question mark to signify that it is not known if the loss of Met1 means that all protein translation is completely prevented or if an abnormal protein is produced using an alternate Met. Although this mutation has not been reported previously to our knowledge, it is expected to be pathogenic. The variant is found in LSME-MITOP panel(s)." -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at