chr6-53269166-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2
The ENST00000542638.5(ELOVL5):c.736G>T(p.Gly246Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0278 in 1,613,836 control chromosomes in the GnomAD database, including 793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 52 hom., cov: 32)
Exomes 𝑓: 0.029 ( 741 hom. )
Consequence
ELOVL5
ENST00000542638.5 stop_gained
ENST00000542638.5 stop_gained
Scores
1
4
Clinical Significance
Conservation
PhyloP100: 0.492
Genes affected
ELOVL5 (HGNC:21308): (ELOVL fatty acid elongase 5) This gene belongs to the ELO family. It is highly expressed in the adrenal gland and testis, and encodes a multi-pass membrane protein that is localized in the endoplasmic reticulum. This protein is involved in the elongation of long-chain polyunsaturated fatty acids. Mutations in this gene have been associated with spinocerebellar ataxia-38 (SCA38). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
PM4
?
Stoplost variant in ENST00000542638.5 Downstream stopcodon found after 47 codons.
BP6
?
Variant 6-53269166-C-A is Benign according to our data. Variant chr6-53269166-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0189 (2884/152216) while in subpopulation NFE AF= 0.0305 (2074/68024). AF 95% confidence interval is 0.0294. There are 52 homozygotes in gnomad4. There are 1319 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2882 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELOVL5 | NM_021814.5 | c.861G>T | p.Leu287= | synonymous_variant | 8/8 | ENST00000304434.11 | |
ELOVL5 | NM_001242830.2 | c.736G>T | p.Gly246Ter | stop_gained | 7/7 | ||
ELOVL5 | NM_001242828.2 | c.942G>T | p.Leu314= | synonymous_variant | 9/9 | ||
ELOVL5 | NM_001301856.2 | c.861G>T | p.Leu287= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELOVL5 | ENST00000542638.5 | c.736G>T | p.Gly246Ter | stop_gained | 7/7 | 1 | |||
ELOVL5 | ENST00000304434.11 | c.861G>T | p.Leu287= | synonymous_variant | 8/8 | 1 | NM_021814.5 | P1 | |
ELOVL5 | ENST00000370918.8 | c.942G>T | p.Leu314= | synonymous_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0189 AC: 2882AN: 152098Hom.: 52 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0189 AC: 4744AN: 251012Hom.: 69 AF XY: 0.0192 AC XY: 2599AN XY: 135692
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GnomAD4 exome AF: 0.0288 AC: 42036AN: 1461620Hom.: 741 Cov.: 31 AF XY: 0.0280 AC XY: 20372AN XY: 727106
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GnomAD4 genome ? AF: 0.0189 AC: 2884AN: 152216Hom.: 52 Cov.: 32 AF XY: 0.0177 AC XY: 1319AN XY: 74420
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ESP6500AA
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252
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2345
Asia WGS
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2022 | See Variant Classification Assertion Criteria. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
D;D;D;D
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at