rs750447828
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_005527.4(HSPA1L):c.515_517del(p.Leu172del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000215 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
HSPA1L
NM_005527.4 inframe_deletion
NM_005527.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.19
Genes affected
HSPA1L (HGNC:5234): (heat shock protein family A (Hsp70) member 1 like) This gene encodes a 70kDa heat shock protein. In conjunction with other heat shock proteins, this protein stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. The gene is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which also encode isoforms of the 70kDa heat shock protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_005527.4. Strenght limited to Supporting due to length of the change: 1aa.
BS2
?
High AC in GnomAd4 at 17 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA1L | NM_005527.4 | c.515_517del | p.Leu172del | inframe_deletion | 2/2 | ENST00000375654.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA1L | ENST00000375654.5 | c.515_517del | p.Leu172del | inframe_deletion | 2/2 | 1 | NM_005527.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152178Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251466Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135914
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GnomAD4 exome AF: 0.000226 AC: 330AN: 1461884Hom.: 0 AF XY: 0.000226 AC XY: 164AN XY: 727246
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GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74344
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Inflammatory bowel disease 1 Other:1
association, no assertion criteria provided | research | Human Development and Health, University of Southampton | Aug 06, 2016 | HSPA1L Dominant negative effects - Our results indicate that de novo and rare mutations in HSPA1L are associated with IBD and provide insights into the pathogenesis of IBD - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at