1-220748772-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017898.5(MTARC2):c.241A>G(p.Met81Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000845 in 1,598,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017898.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTARC2 | NM_017898.5 | c.241A>G | p.Met81Val | missense_variant | 1/8 | ENST00000366913.8 | |
LOC124904516 | XR_007066884.1 | n.44T>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTARC2 | ENST00000366913.8 | c.241A>G | p.Met81Val | missense_variant | 1/8 | 1 | NM_017898.5 | P1 | |
MTARC2 | ENST00000359316.6 | c.241A>G | p.Met81Val | missense_variant | 1/5 | 1 | |||
MTARC2 | ENST00000469583.1 | c.241A>G | p.Met81Val | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000161 AC: 35AN: 217860Hom.: 0 AF XY: 0.000177 AC XY: 21AN XY: 118518
GnomAD4 exome AF: 0.0000857 AC: 124AN: 1446246Hom.: 0 Cov.: 31 AF XY: 0.0000738 AC XY: 53AN XY: 718180
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | The c.241A>G (p.M81V) alteration is located in exon 1 (coding exon 1) of the MARC2 gene. This alteration results from a A to G substitution at nucleotide position 241, causing the methionine (M) at amino acid position 81 to be replaced by a valine (V). 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