chr1-220761679-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_017898.5(MTARC2):c.468A>T(p.Lys156Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,612,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTARC2 | NM_017898.5 | c.468A>T | p.Lys156Asn | missense_variant | 3/8 | ENST00000366913.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTARC2 | ENST00000366913.8 | c.468A>T | p.Lys156Asn | missense_variant | 3/8 | 1 | NM_017898.5 | P1 | |
MTARC2 | ENST00000359316.6 | c.468A>T | p.Lys156Asn | missense_variant | 3/5 | 1 | |||
MTARC2 | ENST00000425560.1 | c.171A>T | p.Lys57Asn | missense_variant | 2/4 | 3 | |||
MTARC2 | ENST00000496078.1 | n.167A>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249950Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135170
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460560Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726626
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.468A>T (p.K156N) alteration is located in exon 3 (coding exon 3) of the MARC2 gene. This alteration results from a A to T substitution at nucleotide position 468, causing the lysine (K) at amino acid position 156 to be replaced by an asparagine (N). 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