rs11680329
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005336.6(HDLBP):c.1732-280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 458,524 control chromosomes in the GnomAD database, including 6,740 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 0.14 ( 1962 hom., cov: 32)
Exomes 𝑓: 0.16 ( 4778 hom. )
Consequence
HDLBP
NM_005336.6 intron
NM_005336.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.53
Genes affected
HDLBP (HGNC:4857): (high density lipoprotein binding protein) The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 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=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDLBP | NM_005336.6 | c.1732-280G>A | intron_variant | ENST00000310931.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDLBP | ENST00000310931.10 | c.1732-280G>A | intron_variant | 1 | NM_005336.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21338AN: 152110Hom.: 1963 Cov.: 32
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GnomAD4 exome AF: 0.159 AC: 48690AN: 306296Hom.: 4778 Cov.: 0 AF XY: 0.153 AC XY: 25003AN XY: 163748
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GnomAD4 genome ? AF: 0.140 AC: 21325AN: 152228Hom.: 1962 Cov.: 32 AF XY: 0.139 AC XY: 10342AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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