chr6-31810752-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_005527.4(HSPA1L):c.1221G>A(p.Thr407=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 1,613,840 control chromosomes in the GnomAD database, including 7,793 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1599 hom., cov: 32)
Exomes 𝑓: 0.080 ( 6194 hom. )
Consequence
HSPA1L
NM_005527.4 synonymous
NM_005527.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -9.35
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 Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 6-31810752-C-T is Benign according to our data. Variant chr6-31810752-C-T is described in ClinVar as [Benign]. Clinvar id is 3059212.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-9.35 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA1L | NM_005527.4 | c.1221G>A | p.Thr407= | synonymous_variant | 2/2 | ENST00000375654.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA1L | ENST00000375654.5 | c.1221G>A | p.Thr407= | synonymous_variant | 2/2 | 1 | NM_005527.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19142AN: 151848Hom.: 1592 Cov.: 32
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GnomAD3 exomes AF: 0.103 AC: 25959AN: 251410Hom.: 1898 AF XY: 0.0982 AC XY: 13342AN XY: 135884
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GnomAD4 exome AF: 0.0800 AC: 116982AN: 1461874Hom.: 6194 Cov.: 37 AF XY: 0.0798 AC XY: 58070AN XY: 727240
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GnomAD4 genome ? AF: 0.126 AC: 19164AN: 151966Hom.: 1599 Cov.: 32 AF XY: 0.125 AC XY: 9286AN XY: 74254
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
HSPA1L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at