chr6-158767377-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001111077.2(EZR):c.1480G>C(p.Ala494Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 1,613,982 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A494V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001111077.2 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 |
---|---|---|---|---|---|---|---|
EZR | NM_001111077.2 | c.1480G>C | p.Ala494Pro | missense_variant | 13/14 | ENST00000367075.4 | |
EZR | NM_003379.5 | c.1480G>C | p.Ala494Pro | missense_variant | 12/13 | ||
EZR | XM_011536110.2 | c.1072G>C | p.Ala358Pro | missense_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EZR | ENST00000367075.4 | c.1480G>C | p.Ala494Pro | missense_variant | 13/14 | 1 | NM_001111077.2 | P1 | |
EZR | ENST00000337147.11 | c.1480G>C | p.Ala494Pro | missense_variant | 12/13 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0161 AC: 2455AN: 152014Hom.: 55 Cov.: 32
GnomAD3 exomes AF: 0.00419 AC: 1052AN: 251286Hom.: 39 AF XY: 0.00324 AC XY: 440AN XY: 135842
GnomAD4 exome AF: 0.00165 AC: 2407AN: 1461850Hom.: 64 Cov.: 40 AF XY: 0.00138 AC XY: 1003AN XY: 727234
GnomAD4 genome ? AF: 0.0161 AC: 2456AN: 152132Hom.: 55 Cov.: 32 AF XY: 0.0157 AC XY: 1171AN XY: 74352
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