chr5-152395583-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020167.5(NMUR2):c.813T>G(p.Phe271Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict 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.813T>G | p.Phe271Leu | missense_variant, splice_region_variant | 3/4 | ENST00000255262.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMUR2 | ENST00000255262.4 | c.813T>G | p.Phe271Leu | missense_variant, splice_region_variant | 3/4 | 1 | NM_020167.5 | P1 | |
ENST00000663819.1 | n.183+20370A>C | intron_variant, non_coding_transcript_variant | |||||||
NMUR2 | ENST00000518933.1 | n.359T>G | splice_region_variant, non_coding_transcript_exon_variant | 4/4 | 3 | ||||
ENST00000663460.1 | n.216+20370A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151924Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250698Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135502
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461230Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726892
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152042Hom.: 0 Cov.: 29 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.813T>G (p.F271L) alteration is located in exon 3 (coding exon 3) of the NMUR2 gene. This alteration results from a T to G substitution at nucleotide position 813, causing the phenylalanine (F) at amino acid position 271 to be replaced by a leucine (L). 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