7-10933700-C-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_002489.4(NDUFA4):c.190-8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NDUFA4
NM_002489.4 splice_region, intron
NM_002489.4 splice_region, intron
Scores
2
Splicing: ADA: 0.00003379
2
Clinical Significance
Conservation
PhyloP100: -1.53
Genes affected
NDUFA4 (HGNC:7687): (NDUFA4 mitochondrial complex associated) The protein encoded by this gene belongs to the complex I 9kDa subunit family. Mammalian complex I of mitochondrial respiratory chain is composed of 45 different subunits. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 7-10933700-C-A is Benign according to our data. Variant chr7-10933700-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2799347.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFA4 | NM_002489.4 | c.190-8G>T | splice_region_variant, intron_variant | Intron 3 of 3 | ENST00000339600.6 | NP_002480.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFA4 | ENST00000339600.6 | c.190-8G>T | splice_region_variant, intron_variant | Intron 3 of 3 | 1 | NM_002489.4 | ENSP00000339720.5 | |||
NDUFA4 | ENST00000470761.5 | n.475-8G>T | splice_region_variant, intron_variant | Intron 3 of 3 | 4 | |||||
NDUFA4 | ENST00000482299.1 | n.429-8G>T | splice_region_variant, intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 151878Hom.: 0 Cov.: 32 FAILED QC
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GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248290Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134458
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.90e-7 AC: 1AN: 1449016Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 721692
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000132 AC: 2AN: 151878Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74188
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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
Oct 19, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at