rs7530493
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022746.4(MTARC1):c.*2940G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 152,170 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00018 ( 1 hom., cov: 32)
Consequence
MTARC1
NM_022746.4 3_prime_UTR
NM_022746.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.111
Genes affected
MTARC1 (HGNC:26189): (mitochondrial amidoxime reducing component 1) Enables molybdenum ion binding activity; molybdopterin cofactor binding activity; and oxidoreductase activity, acting on other nitrogenous compounds as donors. Contributes to nitrite reductase (NO-forming) activity. Involved in cellular detoxification of nitrogen compound; nitrate metabolic process; and nitric oxide biosynthetic process. Located in mitochondrion. Part of nitric-oxide synthase complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTARC1 | ENST00000366910.10 | c.*2940G>A | 3_prime_UTR_variant | Exon 7 of 7 | 1 | NM_022746.4 | ENSP00000355877.5 | |||
ENSG00000286231 | ENST00000651706.1 | n.842+11084G>A | intron_variant | Intron 6 of 8 | ENSP00000499157.1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152052Hom.: 1 Cov.: 32
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GnomAD4 genome AF: 0.000184 AC: 28AN: 152170Hom.: 1 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74388
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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