chr16-21599771-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016025.5(METTL9):c.38C>T(p.Ala13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000596 in 1,542,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016025.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL9 | NM_016025.5 | c.38C>T | p.Ala13Val | missense_variant | 1/5 | ENST00000358154.8 | |
METTL9 | NM_001077180.3 | c.38C>T | p.Ala13Val | missense_variant | 1/5 | ||
METTL9 | NM_001288659.2 | c.45+2471C>T | intron_variant | ||||
METTL9 | NM_001288660.2 | c.45+2471C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL9 | ENST00000358154.8 | c.38C>T | p.Ala13Val | missense_variant | 1/5 | 1 | NM_016025.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151998Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000633 AC: 88AN: 1390866Hom.: 0 Cov.: 33 AF XY: 0.0000709 AC XY: 49AN XY: 690870
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.38C>T (p.A13V) alteration is located in exon 1 (coding exon 1) of the METTL9 gene. This alteration results from a C to T substitution at nucleotide position 38, causing the alanine (A) at amino acid position 13 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