rs6570232
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014320.3(HEBP2):c.419+2376T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,034 control chromosomes in the GnomAD database, including 4,719 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 0.18 ( 4719 hom., cov: 32)
Consequence
HEBP2
NM_014320.3 intron
NM_014320.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.861
Genes affected
HEBP2 (HGNC:15716): (heme binding protein 2) The protein encoded by this gene is found predominately in the cytoplasm, where it plays a role in the collapse of mitochondrial membrane potential (MMP) prior to necrotic cell death. The encoded protein enhances outer and inner mitochondrial membrane permeabilization, especially under conditions of oxidative stress. [provided by RefSeq, May 2016]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HEBP2 | NM_014320.3 | c.419+2376T>C | intron_variant | ENST00000607197.6 | |||
HEBP2 | NM_001326380.2 | c.452+2376T>C | intron_variant | ||||
HEBP2 | NM_001326381.2 | c.301+2494T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HEBP2 | ENST00000607197.6 | c.419+2376T>C | intron_variant | 1 | NM_014320.3 | P1 | |||
HEBP2 | ENST00000367697.7 | c.301+2494T>C | intron_variant | 2 | |||||
HEBP2 | ENST00000448741.5 | c.334+2494T>C | intron_variant | 5 | |||||
HEBP2 | ENST00000453452.1 | c.63+2494T>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 27289AN: 151916Hom.: 4691 Cov.: 32
GnomAD3 genomes
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27289
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.180 AC: 27368AN: 152034Hom.: 4719 Cov.: 32 AF XY: 0.176 AC XY: 13065AN XY: 74330
GnomAD4 genome
?
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152034
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32
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13065
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74330
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373
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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