6-53269247-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000542638.5(ELOVL5):c.655C>T(p.Pro219Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,611,296 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 (★). Synonymous variant affecting the same amino acid position (i.e. P219P) has been classified as Benign.
Frequency
Consequence
ENST00000542638.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELOVL5 | NM_021814.5 | c.780C>T | p.Ser260= | synonymous_variant | 8/8 | ENST00000304434.11 | |
ELOVL5 | NM_001242830.2 | c.655C>T | p.Pro219Ser | missense_variant | 7/7 | ||
ELOVL5 | NM_001242828.2 | c.861C>T | p.Ser287= | synonymous_variant | 9/9 | ||
ELOVL5 | NM_001301856.2 | c.780C>T | p.Ser260= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELOVL5 | ENST00000542638.5 | c.655C>T | p.Pro219Ser | missense_variant | 7/7 | 1 | |||
ELOVL5 | ENST00000304434.11 | c.780C>T | p.Ser260= | synonymous_variant | 8/8 | 1 | NM_021814.5 | P1 | |
ELOVL5 | ENST00000370918.8 | c.861C>T | p.Ser287= | synonymous_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247166Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133780
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1459152Hom.: 0 Cov.: 31 AF XY: 0.0000496 AC XY: 36AN XY: 725882
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at