6-53270677-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000542638.5(ELOVL5):c.547G>A(p.Val183Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000542638.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELOVL5 | NM_021814.5 | c.672G>A | p.Pro224= | synonymous_variant | 7/8 | ENST00000304434.11 | |
ELOVL5 | NM_001242830.2 | c.547G>A | p.Val183Met | missense_variant | 6/7 | ||
ELOVL5 | NM_001242828.2 | c.753G>A | p.Pro251= | synonymous_variant | 8/9 | ||
ELOVL5 | NM_001301856.2 | c.672G>A | p.Pro224= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELOVL5 | ENST00000542638.5 | c.547G>A | p.Val183Met | missense_variant | 6/7 | 1 | |||
ELOVL5 | ENST00000304434.11 | c.672G>A | p.Pro224= | synonymous_variant | 7/8 | 1 | NM_021814.5 | P1 | |
ELOVL5 | ENST00000370918.8 | c.753G>A | p.Pro251= | synonymous_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251192Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135748
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 727216
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at