16-23690838-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033266.4(ERN2):c.2774G>A(p.Gly925Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,610,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033266.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERN2 | NM_033266.4 | c.2774G>A | p.Gly925Glu | missense_variant | Exon 22 of 22 | ENST00000256797.9 | NP_150296.4 | |
ERN2 | NM_001308220.2 | c.2618G>A | p.Gly873Glu | missense_variant | Exon 21 of 21 | NP_001295149.2 | ||
ERN2 | XM_047433506.1 | c.2342G>A | p.Gly781Glu | missense_variant | Exon 19 of 19 | XP_047289462.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERN2 | ENST00000256797.9 | c.2774G>A | p.Gly925Glu | missense_variant | Exon 22 of 22 | 1 | NM_033266.4 | ENSP00000256797.5 | ||
ERN2 | ENST00000457008.6 | c.2618G>A | p.Gly873Glu | missense_variant | Exon 21 of 21 | 1 | ENSP00000413812.2 | |||
ERN2 | ENST00000562458.2 | n.*487G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 | ENSP00000456866.2 | ||||
ERN2 | ENST00000562458.2 | n.*487G>A | 3_prime_UTR_variant | Exon 5 of 5 | 3 | ENSP00000456866.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000567 AC: 14AN: 247004Hom.: 0 AF XY: 0.0000598 AC XY: 8AN XY: 133826
GnomAD4 exome AF: 0.000146 AC: 213AN: 1458522Hom.: 0 Cov.: 33 AF XY: 0.000145 AC XY: 105AN XY: 725678
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2774G>A (p.G925D) alteration is located in exon 22 (coding exon 22) of the ERN2 gene. This alteration results from a G to A substitution at nucleotide position 2774, causing the glycine (G) at amino acid position 925 to be replaced by an aspartic acid (D). 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