NM_024306.5:c.925G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024306.5(FA2H):c.925G>A(p.Val309Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024306.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FA2H | NM_024306.5 | c.925G>A | p.Val309Ile | missense_variant | Exon 6 of 7 | ENST00000219368.8 | NP_077282.3 | |
FA2H | XM_011523319.3 | c.685G>A | p.Val229Ile | missense_variant | Exon 6 of 7 | XP_011521621.1 | ||
FA2H | XM_011523317.4 | c.*1789G>A | 3_prime_UTR_variant | Exon 6 of 6 | XP_011521619.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FA2H | ENST00000219368.8 | c.925G>A | p.Val309Ile | missense_variant | Exon 6 of 7 | 1 | NM_024306.5 | ENSP00000219368.3 | ||
FA2H | ENST00000562145.1 | n.646G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
FA2H | ENST00000567683.5 | n.*204G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 | ENSP00000455126.1 | ||||
FA2H | ENST00000567683.5 | n.*204G>A | 3_prime_UTR_variant | Exon 4 of 5 | 2 | ENSP00000455126.1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 151954Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000211 AC: 53AN: 251198Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135790
GnomAD4 exome AF: 0.000159 AC: 232AN: 1461866Hom.: 0 Cov.: 30 AF XY: 0.000155 AC XY: 113AN XY: 727234
GnomAD4 genome AF: 0.000184 AC: 28AN: 152072Hom.: 0 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74338
ClinVar
Submissions by phenotype
not provided Uncertain:5
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
BP4 -
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FA2H: PM2, BP4 -
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not specified Uncertain:1
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Hereditary spastic paraplegia Uncertain:1
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Spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at