rs2074897
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024407.5(NDUFS7):c.455+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,539,078 control chromosomes in the GnomAD database, including 158,271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.35 ( 11075 hom., cov: 31)
Exomes 𝑓: 0.46 ( 147196 hom. )
Consequence
NDUFS7
NM_024407.5 intron
NM_024407.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.741
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 19-1391236-G-A is Benign according to our data. Variant chr19-1391236-G-A is described in ClinVar as [Benign]. Clinvar id is 1185398.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFS7 | NM_024407.5 | c.455+71G>A | intron_variant | ENST00000233627.14 | NP_077718.3 | |||
NDUFS7 | NM_001363602.2 | c.455+71G>A | intron_variant | NP_001350531.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFS7 | ENST00000233627.14 | c.455+71G>A | intron_variant | 1 | NM_024407.5 | ENSP00000233627.9 |
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52740AN: 151828Hom.: 11078 Cov.: 31
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GnomAD4 exome AF: 0.455 AC: 631212AN: 1387130Hom.: 147196 AF XY: 0.456 AC XY: 313328AN XY: 687570
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GnomAD4 genome AF: 0.347 AC: 52730AN: 151948Hom.: 11075 Cov.: 31 AF XY: 0.343 AC XY: 25470AN XY: 74242
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Mitochondrial complex 1 deficiency, nuclear type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at