15-34350804-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001284292.2(NUTM1):c.910C>T(p.Arg304Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R304Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001284292.2 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 |
---|---|---|---|---|---|---|---|
NUTM1 | NM_001284292.2 | c.910C>T | p.Arg304Trp | missense_variant | 4/8 | ENST00000537011.6 | |
NUTM1 | NM_001284293.2 | c.880C>T | p.Arg294Trp | missense_variant | 3/7 | ||
NUTM1 | NM_175741.3 | c.826C>T | p.Arg276Trp | missense_variant | 4/8 | ||
NUTM1 | XM_047432341.1 | c.826C>T | p.Arg276Trp | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUTM1 | ENST00000537011.6 | c.910C>T | p.Arg304Trp | missense_variant | 4/8 | 2 | NM_001284292.2 | A2 | |
NUTM1 | ENST00000333756.5 | c.826C>T | p.Arg276Trp | missense_variant | 4/8 | 1 | P2 | ||
NUTM1 | ENST00000438749.7 | c.880C>T | p.Arg294Trp | missense_variant | 3/7 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251366Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135848
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727188
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.826C>T (p.R276W) alteration is located in exon 3 (coding exon 3) of the NUTM1 gene. This alteration results from a C to T substitution at nucleotide position 826, causing the arginine (R) at amino acid position 276 to be replaced by a tryptophan (W). 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