NM_004134.7:c.1426G>A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BS1_SupportingBS2
The NM_004134.7(HSPA9):c.1426G>A(p.Ala476Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00036 in 1,611,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_004134.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPA9 | NM_004134.7 | c.1426G>A | p.Ala476Thr | missense_variant | Exon 12 of 17 | ENST00000297185.9 | NP_004125.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000358 AC: 90AN: 251370Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135866
GnomAD4 exome AF: 0.000363 AC: 530AN: 1459828Hom.: 0 Cov.: 29 AF XY: 0.000359 AC XY: 261AN XY: 726334
GnomAD4 genome AF: 0.000329 AC: 50AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74244
ClinVar
Submissions by phenotype
not provided Uncertain:3
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HSPA9-related disorder Uncertain:1
The HSPA9 c.1426G>A variant is predicted to result in the amino acid substitution p.Ala476Thr. This variant was reported in an individual with sporadic Parkinson disease (Burbulla et al. 2010. PubMed ID: 20817635). This variant is reported in 0.080% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-137894331-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at