2-197487056-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_002156.5(HSPD1):c.1712G>T(p.Gly571Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000476 in 1,470,368 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002156.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPD1 | NM_002156.5 | c.1712G>T | p.Gly571Val | missense_variant | Exon 12 of 12 | ENST00000388968.8 | NP_002147.2 | |
HSPD1 | NM_199440.2 | c.1712G>T | p.Gly571Val | missense_variant | Exon 12 of 12 | NP_955472.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152016Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000812 AC: 20AN: 246414Hom.: 0 AF XY: 0.0000670 AC XY: 9AN XY: 134244
GnomAD4 exome AF: 0.0000266 AC: 35AN: 1318234Hom.: 0 Cov.: 20 AF XY: 0.0000211 AC XY: 14AN XY: 663402
GnomAD4 genome AF: 0.000230 AC: 35AN: 152134Hom.: 1 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74356
ClinVar
Submissions by phenotype
Hypomyelinating leukodystrophy 4 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at