chr13-31148483-T-TAAAA
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006644.4(HSPH1):c.1138-4_1138-3insTTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
HSPH1
NM_006644.4 splice_region, splice_polypyrimidine_tract, intron
NM_006644.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.36
Genes affected
HSPH1 (HGNC:16969): (heat shock protein family H (Hsp110) member 1) This gene encodes a member of the heat shock protein 70 family of proteins. The encoded protein functions as a nucleotide exchange factor for the molecular chaperone heat shock cognate 71 kDa protein (Hsc70). In addition, this protein plays a distinct but related role as a holdase that inhibits the aggregation of misfolded proteins, including the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Elevated expression of this protein has been observed in numerous human cancers. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPH1 | NM_006644.4 | c.1138-4_1138-3insTTTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000320027.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPH1 | ENST00000320027.10 | c.1138-4_1138-3insTTTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006644.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
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0
GnomAD4 exome AF: 0.0000104 AC: 9AN: 866378Hom.: 0 Cov.: 0 AF XY: 0.00000919 AC XY: 4AN XY: 435040
GnomAD4 exome
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9
AN:
866378
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0
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4
AN XY:
435040
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GnomAD4 genome Cov.: 0
GnomAD4 genome
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0
ClinVar
Not reported inComputational scores
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Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at