21-28879908-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013240.6(N6AMT1):c.358G>A(p.Val120Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00008 in 1,599,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013240.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
N6AMT1 | NM_013240.6 | c.358G>A | p.Val120Met | missense_variant | Exon 4 of 6 | ENST00000303775.10 | NP_037372.4 | |
N6AMT1 | NM_182749.5 | c.313-1575G>A | intron_variant | Intron 3 of 4 | NP_877426.4 | |||
N6AMT1 | NR_047510.3 | n.380G>A | non_coding_transcript_exon_variant | Exon 4 of 7 | ||||
N6AMT1 | XR_007067787.1 | n.380G>A | non_coding_transcript_exon_variant | Exon 4 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
N6AMT1 | ENST00000303775.10 | c.358G>A | p.Val120Met | missense_variant | Exon 4 of 6 | 1 | NM_013240.6 | ENSP00000303584.5 | ||
N6AMT1 | ENST00000351429.7 | c.313-1575G>A | intron_variant | Intron 3 of 4 | 1 | ENSP00000286764.4 | ||||
N6AMT1 | ENST00000460212.1 | n.358G>A | non_coding_transcript_exon_variant | Exon 4 of 7 | 1 | ENSP00000436490.1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152090Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000134 AC: 33AN: 245556Hom.: 0 AF XY: 0.000158 AC XY: 21AN XY: 133050
GnomAD4 exome AF: 0.0000816 AC: 118AN: 1446942Hom.: 0 Cov.: 30 AF XY: 0.0000973 AC XY: 70AN XY: 719676
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.358G>A (p.V120M) alteration is located in exon 4 (coding exon 4) of the N6AMT1 gene. This alteration results from a G to A substitution at nucleotide position 358, causing the valine (V) at amino acid position 120 to be replaced by a methionine (M). 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