rs200535861
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003640.5(ELP1):c.1656G>T(p.Ala552=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A552A) has been classified as Likely benign.
Frequency
Consequence
NM_003640.5 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 |
---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.1656G>T | p.Ala552= | synonymous_variant | 15/37 | ENST00000374647.10 | |
ELP1 | NM_001318360.2 | c.1314G>T | p.Ala438= | synonymous_variant | 15/37 | ||
ELP1 | NM_001330749.2 | c.609G>T | p.Ala203= | synonymous_variant | 13/35 | ||
ELP1 | XM_047423991.1 | c.1656G>T | p.Ala552= | synonymous_variant | 15/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.1656G>T | p.Ala552= | synonymous_variant | 15/37 | 1 | NM_003640.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 11, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.