rs6705421
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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.-102-4716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 984,306 control chromosomes in the GnomAD database, including 151,852 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 0.52 ( 21600 hom., cov: 30)
Exomes 𝑓: 0.56 ( 130252 hom. )
Consequence
HDLBP
NM_005336.6 intron
NM_005336.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.60
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=-0.97).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDLBP | NM_005336.6 | c.-102-4716T>C | intron_variant | ENST00000310931.10 | |||
HDLBP-AS1 | NR_168372.1 | n.1094A>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDLBP | ENST00000310931.10 | c.-102-4716T>C | intron_variant | 1 | NM_005336.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.522 AC: 79340AN: 151868Hom.: 21553 Cov.: 30
GnomAD3 genomes
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GnomAD4 exome AF: 0.558 AC: 464836AN: 832320Hom.: 130252 Cov.: 24 AF XY: 0.558 AC XY: 214308AN XY: 384408
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GnomAD4 genome ? AF: 0.523 AC: 79437AN: 151986Hom.: 21600 Cov.: 30 AF XY: 0.526 AC XY: 39066AN XY: 74276
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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