rs774354874
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000158.4(GBE1):āc.1842T>Cā(p.Ile614=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. I614I) has been classified as Likely benign.
Frequency
Consequence
NM_000158.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBE1 | NM_000158.4 | c.1842T>C | p.Ile614= | synonymous_variant | 14/16 | ENST00000429644.7 | |
GBE1 | XR_007095662.1 | n.1970T>C | non_coding_transcript_exon_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBE1 | ENST00000429644.7 | c.1842T>C | p.Ile614= | synonymous_variant | 14/16 | 1 | NM_000158.4 | P1 | |
GBE1 | ENST00000489715.1 | c.1719T>C | p.Ile573= | synonymous_variant | 14/16 | 2 | |||
GBE1 | ENST00000484687.1 | n.243T>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247122Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134158
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459196Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725912
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at