NM_015938.5:c.907C>T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015938.5(NMD3):c.907C>T(p.Pro303Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015938.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMD3 | ENST00000351193.7 | c.907C>T | p.Pro303Ser | missense_variant | Exon 11 of 16 | 1 | NM_015938.5 | ENSP00000307525.2 | ||
NMD3 | ENST00000472947.5 | c.907C>T | p.Pro303Ser | missense_variant | Exon 11 of 17 | 1 | ENSP00000417559.1 | |||
NMD3 | ENST00000460469.1 | c.907C>T | p.Pro303Ser | missense_variant | Exon 10 of 15 | 1 | ENSP00000419004.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151972Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251216Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135776
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461174Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726912
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74210
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.907C>T (p.P303S) alteration is located in exon 11 (coding exon 10) of the NMD3 gene. This alteration results from a C to T substitution at nucleotide position 907, causing the proline (P) at amino acid position 303 to be replaced by a serine (S). 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