18-2544270-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022840.5(METTL4):c.1198G>A(p.Val400Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,611,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022840.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METTL4 | NM_022840.5 | c.1198G>A | p.Val400Met | missense_variant | 8/9 | ENST00000574538.2 | NP_073751.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METTL4 | ENST00000574538.2 | c.1198G>A | p.Val400Met | missense_variant | 8/9 | 1 | NM_022840.5 | ENSP00000458290.1 | ||
METTL4 | ENST00000573134.1 | n.3499G>A | non_coding_transcript_exon_variant | 6/7 | 1 | |||||
METTL4 | ENST00000319888.10 | c.1181+383G>A | intron_variant | 5 | ENSP00000320349.6 | |||||
METTL4 | ENST00000576251.5 | c.267+3085G>A | intron_variant | 2 | ENSP00000460774.1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151976Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250304Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135348
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1459864Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 14AN XY: 726310
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151976Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74204
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.1198G>A (p.V400M) alteration is located in exon 8 (coding exon 7) of the METTL4 gene. This alteration results from a G to A substitution at nucleotide position 1198, causing the valine (V) at amino acid position 400 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