rs6076550
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_052970.5(HSPA12B):c.562C>T(p.Leu188=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0181 in 1,613,808 control chromosomes in the GnomAD database, including 328 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 0.018 ( 22 hom., cov: 32)
Exomes 𝑓: 0.018 ( 306 hom. )
Consequence
HSPA12B
NM_052970.5 synonymous
NM_052970.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.00
Genes affected
HSPA12B (HGNC:16193): (heat shock protein family A (Hsp70) member 12B) The protein encoded by this gene contains an atypical heat shock protein 70 (Hsp70) ATPase domain and is therefore a distant member of the mammalian Hsp70 family. This gene may be involved in susceptibility to atherosclerosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.018 (2744/152356) while in subpopulation SAS AF= 0.0276 (133/4822). AF 95% confidence interval is 0.0238. There are 22 homozygotes in gnomad4. There are 1305 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 22 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA12B | NM_052970.5 | c.562C>T | p.Leu188= | synonymous_variant | 7/13 | ENST00000254963.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA12B | ENST00000254963.7 | c.562C>T | p.Leu188= | synonymous_variant | 7/13 | 1 | NM_052970.5 | P1 | |
HSPA12B | ENST00000399701.1 | c.304C>T | p.Leu102= | synonymous_variant | 6/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0180 AC: 2740AN: 152238Hom.: 22 Cov.: 32
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GnomAD3 exomes AF: 0.0182 AC: 4584AN: 251336Hom.: 57 AF XY: 0.0188 AC XY: 2557AN XY: 135864
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GnomAD4 exome AF: 0.0181 AC: 26444AN: 1461452Hom.: 306 Cov.: 32 AF XY: 0.0184 AC XY: 13399AN XY: 727054
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GnomAD4 genome ? AF: 0.0180 AC: 2744AN: 152356Hom.: 22 Cov.: 32 AF XY: 0.0175 AC XY: 1305AN XY: 74504
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ClinVar
Not reported inComputational scores
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Name
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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