6-10983803-A-G
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017770.4(ELOVL2):c.869T>C(p.Val290Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,609,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017770.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELOVL2 | NM_017770.4 | c.869T>C | p.Val290Ala | missense_variant | Exon 8 of 8 | ENST00000354666.4 | NP_060240.3 | |
ELOVL2 | XM_011514716.4 | c.959T>C | p.Val320Ala | missense_variant | Exon 8 of 8 | XP_011513018.1 | ||
ELOVL2 | XM_011514717.4 | c.872T>C | p.Val291Ala | missense_variant | Exon 8 of 8 | XP_011513019.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151830Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000726 AC: 18AN: 247764 AF XY: 0.0000672 show subpopulations
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1457718Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725060 show subpopulations
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151830Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74130 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.869T>C (p.V290A) alteration is located in exon 8 (coding exon 8) of the ELOVL2 gene. This alteration results from a T to C substitution at nucleotide position 869, causing the valine (V) at amino acid position 290 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at