1-220796728-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_022746.4(MTARC1):c.535C>T(p.Arg179Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,612,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022746.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTARC1 | ENST00000366910.10 | c.535C>T | p.Arg179Cys | missense_variant | Exon 3 of 7 | 1 | NM_022746.4 | ENSP00000355877.5 | ||
ENSG00000286231 | ENST00000651706.1 | n.490C>T | non_coding_transcript_exon_variant | Exon 3 of 9 | ENSP00000499157.1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249182Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134776
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1460562Hom.: 0 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 726584
GnomAD4 genome AF: 0.000131 AC: 20AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.535C>T (p.R179C) alteration is located in exon 3 (coding exon 3) of the MARC1 gene. This alteration results from a C to T substitution at nucleotide position 535, causing the arginine (R) at amino acid position 179 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at