chr2-158115152-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_173355.4(UPP2):āc.232A>Cā(p.Met78Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00115 in 1,613,812 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_173355.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPP2 | NM_173355.4 | c.232A>C | p.Met78Leu | missense_variant | 3/7 | ENST00000005756.5 | |
UPP2 | NM_001135098.2 | c.403A>C | p.Met135Leu | missense_variant | 5/9 | ||
UPP2 | XM_017003484.2 | c.232A>C | p.Met78Leu | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPP2 | ENST00000005756.5 | c.232A>C | p.Met78Leu | missense_variant | 3/7 | 1 | NM_173355.4 | P1 | |
UPP2 | ENST00000605860.5 | c.403A>C | p.Met135Leu | missense_variant | 6/10 | 5 | |||
UPP2 | ENST00000460456.1 | n.377-8597A>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00539 AC: 820AN: 152118Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00162 AC: 407AN: 250808Hom.: 3 AF XY: 0.00114 AC XY: 154AN XY: 135532
GnomAD4 exome AF: 0.000709 AC: 1036AN: 1461576Hom.: 3 Cov.: 30 AF XY: 0.000626 AC XY: 455AN XY: 727106
GnomAD4 genome AF: 0.00540 AC: 822AN: 152236Hom.: 7 Cov.: 32 AF XY: 0.00540 AC XY: 402AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at