19-8321175-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_005001.5(NDUFA7):c.51+133A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,178,274 control chromosomes in the GnomAD database, including 8,063 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.15 ( 3813 hom., cov: 32)
Exomes 𝑓: 0.056 ( 4250 hom. )
Consequence
NDUFA7
NM_005001.5 intron
NM_005001.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.989
Genes affected
NDUFA7 (HGNC:7691): (NADH:ubiquinone oxidoreductase subunit A7) This gene encodes a subunit of NADH:ubiquinone oxidoreductase (complex I), which is a multiprotein complex located in the inner mitochondrial membrane. Complex I functions in the transfer of electrons from NADH to the respiratory chain. [provided by RefSeq, Mar 2011]
RPS28 (HGNC:10418): (ribosomal protein S28) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S28E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 19-8321175-T-G is Benign according to our data. Variant chr19-8321175-T-G is described in ClinVar as [Benign]. Clinvar id is 1265048.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA7 | NM_005001.5 | c.51+133A>C | intron_variant | ENST00000301457.3 | |||
NDUFA7 | NR_135539.2 | n.68+133A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA7 | ENST00000301457.3 | c.51+133A>C | intron_variant | 1 | NM_005001.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.151 AC: 22910AN: 151614Hom.: 3795 Cov.: 32
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GnomAD4 exome AF: 0.0559 AC: 57371AN: 1026542Hom.: 4250 Cov.: 14 AF XY: 0.0590 AC XY: 29875AN XY: 506292
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GnomAD4 genome ? AF: 0.151 AC: 22970AN: 151732Hom.: 3813 Cov.: 32 AF XY: 0.152 AC XY: 11276AN XY: 74186
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
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