chr5-152398090-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020167.5(NMUR2):c.781C>A(p.Pro261Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020167.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.781C>A | p.Pro261Thr | missense_variant | 2/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.781C>A | p.Pro261Thr | missense_variant | 2/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+22877G>T | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.327C>A | non_coding_transcript_exon_variant | 3/4 | 3 | ||||
ENST00000663460.1 | n.216+22877G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250662Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135544
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1461056Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726844
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 23, 2021 | The c.781C>A (p.P261T) alteration is located in exon 2 (coding exon 2) of the NMUR2 gene. This alteration results from a C to A substitution at nucleotide position 781, causing the proline (P) at amino acid position 261 to be replaced by a threonine (T). 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