rs797045563
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_007175.8(ERLIN2):c.1002_1007del(p.Ala335_Thr336del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,854 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. T334T) has been classified as Likely benign.
Frequency
Consequence
NM_007175.8 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERLIN2 | NM_007175.8 | c.1002_1007del | p.Ala335_Thr336del | inframe_deletion | 12/12 | ENST00000519638.3 | |
ERLIN2 | NM_001362878.2 | c.1002_1007del | p.Ala335_Thr336del | inframe_deletion | 12/12 | ||
ERLIN2 | XM_047421307.1 | c.1002_1007del | p.Ala335_Thr336del | inframe_deletion | 13/13 | ||
ERLIN2 | XM_047421308.1 | c.756_761del | p.Ala253_Thr254del | inframe_deletion | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERLIN2 | ENST00000519638.3 | c.1002_1007del | p.Ala335_Thr336del | inframe_deletion | 12/12 | 2 | NM_007175.8 | P1 | |
ERLIN2 | ENST00000521644.5 | c.1002_1007del | p.Ala335_Thr336del | inframe_deletion | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251292Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135836
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461670Hom.: 0 AF XY: 0.00000963 AC XY: 7AN XY: 727146
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 12, 2015 | - - |
Spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 03, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 210957). This variant has not been reported in the literature in individuals affected with ERLIN2-related conditions. This variant is present in population databases (rs797045563, gnomAD 0.0009%). This variant, c.1002_1007del, results in the deletion of 2 amino acid(s) of the ERLIN2 protein (p.Ala335_Thr336del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at