rs11807575
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014424.5(HSPB7):c.387G>A(p.Pro129=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,611,576 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 36 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 30 hom. )
Consequence
HSPB7
NM_014424.5 synonymous
NM_014424.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.73
Genes affected
HSPB7 (HGNC:5249): (heat shock protein family B (small) member 7) This gene encodes a small heat shock family B member that can heterodimerize with similar heat shock proteins. Defects in this gene are associated with advanced heart failure. In addition, the encoded protein may be a tumor suppressor in the p53 pathway, with defects in this gene being associated with renal cell carcinoma. [provided by RefSeq, Mar 2017]
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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=-0.84).
BP6
?
Variant 1-16015706-C-T is Benign according to our data. Variant chr1-16015706-C-T is described in ClinVar as [Benign]. Clinvar id is 787740.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.73 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0107 (1624/152306) while in subpopulation AFR AF= 0.0367 (1525/41564). AF 95% confidence interval is 0.0352. There are 36 homozygotes in gnomad4. There are 747 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 36 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPB7 | NM_014424.5 | c.387G>A | p.Pro129= | synonymous_variant | 3/3 | ENST00000311890.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPB7 | ENST00000311890.14 | c.387G>A | p.Pro129= | synonymous_variant | 3/3 | 1 | NM_014424.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0106 AC: 1618AN: 152188Hom.: 36 Cov.: 32
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GnomAD3 exomes AF: 0.00282 AC: 702AN: 248952Hom.: 18 AF XY: 0.00203 AC XY: 273AN XY: 134644
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GnomAD4 exome AF: 0.00107 AC: 1562AN: 1459270Hom.: 30 Cov.: 30 AF XY: 0.000908 AC XY: 659AN XY: 725702
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GnomAD4 genome ? AF: 0.0107 AC: 1624AN: 152306Hom.: 36 Cov.: 32 AF XY: 0.0100 AC XY: 747AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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