rs8523
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_017770.4(ELOVL2):c.*2961C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,466 control chromosomes in the GnomAD database, including 22,598 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 22557 hom., cov: 32)
Exomes 𝑓: 0.45 ( 41 hom. )
Consequence
ELOVL2
NM_017770.4 3_prime_UTR
NM_017770.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.80
Genes affected
ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELOVL2 | NM_017770.4 | c.*2961C>T | 3_prime_UTR_variant | 8/8 | ENST00000354666.4 | ||
ELOVL2 | XM_011514716.4 | c.*2961C>T | 3_prime_UTR_variant | 8/8 | |||
ELOVL2 | XM_011514717.4 | c.*2961C>T | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELOVL2 | ENST00000354666.4 | c.*2961C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_017770.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.532 AC: 80827AN: 151918Hom.: 22519 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.449 AC: 193AN: 430Hom.: 41 Cov.: 0 AF XY: 0.438 AC XY: 113AN XY: 258
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GnomAD4 genome ? AF: 0.532 AC: 80919AN: 152036Hom.: 22557 Cov.: 32 AF XY: 0.540 AC XY: 40164AN XY: 74312
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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