11-123058916-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000526686.1(HSPA8):c.-107T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,428,906 control chromosomes in the GnomAD database, including 300,336 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.71 ( 39732 hom., cov: 33)
Exomes 𝑓: 0.64 ( 260604 hom. )
Consequence
HSPA8
ENST00000526686.1 5_prime_UTR
ENST00000526686.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.74
Genes affected
HSPA8 (HGNC:5241): (heat shock protein family A (Hsp70) member 8) This gene encodes a member of the heat shock protein 70 family, which contains both heat-inducible and constitutively expressed members. This protein belongs to the latter group, which are also referred to as heat-shock cognate proteins. It functions as a chaperone, and binds to nascent polypeptides to facilitate correct folding. It also functions as an ATPase in the disassembly of clathrin-coated vesicles during transport of membrane components through the cell. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA8 | NM_006597.6 | c.1324-86T>C | intron_variant | ENST00000534624.6 | |||
SNORD14D | NR_001454.2 | n.80T>C | non_coding_transcript_exon_variant | 1/1 | |||
HSPA8 | NM_153201.4 | c.1324-86T>C | intron_variant | ||||
HSPA8 | XM_011542798.2 | c.1324-86T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA8 | ENST00000534624.6 | c.1324-86T>C | intron_variant | 1 | NM_006597.6 | P1 | |||
SNORD14D | ENST00000384390.1 | n.80T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.709 AC: 107901AN: 152092Hom.: 39675 Cov.: 33
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GnomAD4 exome AF: 0.636 AC: 812399AN: 1276696Hom.: 260604 Cov.: 17 AF XY: 0.635 AC XY: 407542AN XY: 641550
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GnomAD4 genome AF: 0.710 AC: 108020AN: 152210Hom.: 39732 Cov.: 33 AF XY: 0.704 AC XY: 52398AN XY: 74400
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at