rs776425415
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002156.5(HSPD1):c.*16T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,194,532 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_002156.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSPD1 | NM_002156.5 | c.*16T>C | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000388968.8 | NP_002147.2 | ||
HSPD1 | NM_199440.2 | c.*16T>C | 3_prime_UTR_variant | Exon 12 of 12 | NP_955472.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 151998Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000287 AC: 7AN: 244266Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133276
GnomAD4 exome AF: 0.000113 AC: 118AN: 1042534Hom.: 0 Cov.: 14 AF XY: 0.0000970 AC XY: 52AN XY: 536354
GnomAD4 genome AF: 0.000138 AC: 21AN: 151998Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: HSPD1 c.*16T>C is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 2.9e-05 in 244266 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.*16T>C in individuals affected with HSPD1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at