chr5-152398062-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020167.5(NMUR2):c.809T>C(p.Leu270Pro) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000336 in 1,610,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020167.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
NMUR2 | NM_020167.5 | c.809T>C | p.Leu270Pro | missense_variant, splice_region_variant | 2/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.809T>C | p.Leu270Pro | missense_variant, splice_region_variant | 2/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+22849A>G | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.355T>C | splice_region_variant, non_coding_transcript_exon_variant | 3/4 | 3 | ||||
ENST00000663460.1 | n.216+22849A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000611 AC: 93AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000192 AC: 48AN: 250362Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135342
GnomAD4 exome AF: 0.000307 AC: 448AN: 1458746Hom.: 0 Cov.: 29 AF XY: 0.000313 AC XY: 227AN XY: 725818
GnomAD4 genome ? AF: 0.000611 AC: 93AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000592 AC XY: 44AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.809T>C (p.L270P) alteration is located in exon 2 (coding exon 2) of the NMUR2 gene. This alteration results from a T to C substitution at nucleotide position 809, causing the leucine (L) at amino acid position 270 to be replaced by a proline (P). 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