2-197487066-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_002156.5(HSPD1):c.1702A>G(p.Met568Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000464 in 1,508,944 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002156.5 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 |
---|---|---|---|---|---|---|---|---|
HSPD1 | NM_002156.5 | c.1702A>G | p.Met568Val | missense_variant | Exon 12 of 12 | ENST00000388968.8 | NP_002147.2 | |
HSPD1 | NM_199440.2 | c.1702A>G | p.Met568Val | missense_variant | Exon 12 of 12 | NP_955472.1 | ||
SNORA105B | NR_132788.1 | n.-163A>G | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246882Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134460
GnomAD4 exome AF: 0.00000368 AC: 5AN: 1356874Hom.: 0 Cov.: 21 AF XY: 0.00000587 AC XY: 4AN XY: 680940
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
Spastic paraplegia Uncertain:1
This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 568 of the HSPD1 protein (p.Met568Val). This variant is present in population databases (rs757331948, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with HSPD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1415601). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at