chr6-158767020-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001111077.2(EZR):c.1655T>A(p.Ile552Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I552V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001111077.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EZR | NM_001111077.2 | c.1655T>A | p.Ile552Asn | missense_variant | 14/14 | ENST00000367075.4 | |
EZR | NM_003379.5 | c.1655T>A | p.Ile552Asn | missense_variant | 13/13 | ||
EZR | XM_011536110.2 | c.1247T>A | p.Ile416Asn | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EZR | ENST00000367075.4 | c.1655T>A | p.Ile552Asn | missense_variant | 14/14 | 1 | NM_001111077.2 | P1 | |
EZR | ENST00000337147.11 | c.1655T>A | p.Ile552Asn | missense_variant | 13/13 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251196Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135818
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.1655T>A (p.I552N) alteration is located in exon 13 (coding exon 13) of the EZR gene. This alteration results from a T to A substitution at nucleotide position 1655, causing the isoleucine (I) at amino acid position 552 to be replaced by an asparagine (N). 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