chr11-78069900-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004549.6(NDUFC2):c.*87T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
NDUFC2
NM_004549.6 3_prime_UTR
NM_004549.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.392
Genes affected
NDUFC2 (HGNC:7706): (NADH:ubiquinone oxidoreductase subunit C2) Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrion. Part of mitochondrial respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 11-78069900-A-G is Benign according to our data. Variant chr11-78069900-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3026373.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFC2 | NM_004549.6 | c.*87T>C | 3_prime_UTR_variant | 3/3 | ENST00000281031.5 | ||
NDUFC2-KCTD14 | NM_001203262.2 | c.166+9679T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFC2 | ENST00000281031.5 | c.*87T>C | 3_prime_UTR_variant | 3/3 | 1 | NM_004549.6 | P1 | ||
NDUFC2 | ENST00000527806.1 | c.240T>C | p.Tyr80= | synonymous_variant | 3/3 | 2 | |||
NDUFC2 | ENST00000525085.1 | c.*87T>C | 3_prime_UTR_variant | 3/3 | 3 | ||||
NDUFC2 | ENST00000534029.5 | c.*87T>C | 3_prime_UTR_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460868Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726614
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74382
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | NDUFC2: PM2:Supporting, BP4, BP7 - |
Computational scores
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Name
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Benign
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at