rs768544624
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_024407.5(NDUFS7):c.16+25_16+40delGTGGGGCCGCGCGGGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000192 in 1,563,202 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
NDUFS7
NM_024407.5 intron
NM_024407.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.38
Genes affected
NDUFS7 (HGNC:7714): (NADH:ubiquinone oxidoreductase core subunit S7) This gene encodes a protein that is a subunit of one of the complexes that forms the mitochondrial respiratory chain. This protein is one of over 40 subunits found in complex I, the nicotinamide adenine dinucleotide (NADH):ubiquinone oxidoreductase. This complex functions in the transfer of electrons from NADH to the respiratory chain, and ubiquinone is believed to be the immediate electron acceptor for the enzyme. Mutations in this gene cause Leigh syndrome due to mitochondrial complex I deficiency, a severe neurological disorder that results in bilaterally symmetrical necrotic lesions in subcortical brain regions. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 19-1383960-GGCGGGTGTGGGGCCGC-G is Benign according to our data. Variant chr19-1383960-GGCGGGTGTGGGGCCGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 2872884.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NDUFS7 | NM_024407.5 | c.16+25_16+40delGTGGGGCCGCGCGGGT | intron_variant | Intron 1 of 7 | ENST00000233627.14 | NP_077718.3 | ||
| NDUFS7 | NM_001363602.2 | c.16+25_16+40delGTGGGGCCGCGCGGGT | intron_variant | Intron 1 of 7 | NP_001350531.1 | |||
| NDUFS7 | XM_017026768.3 | c.16+25_16+40delGTGGGGCCGCGCGGGT | intron_variant | Intron 1 of 3 | XP_016882257.2 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1410964Hom.: 0 AF XY: 0.00000143 AC XY: 1AN XY: 697552
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GnomAD4 genome 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 20, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at