2-241230213-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005336.6(HDLBP):c.3531G>A(p.Thr1177=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,613,234 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 1 hom. )
Consequence
HDLBP
NM_005336.6 synonymous
NM_005336.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
Variant 2-241230213-C-T is Benign according to our data. Variant chr2-241230213-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 742799.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
BS2
?
High AC in GnomAd at 29 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDLBP | NM_005336.6 | c.3531G>A | p.Thr1177= | synonymous_variant | 26/28 | ENST00000310931.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDLBP | ENST00000310931.10 | c.3531G>A | p.Thr1177= | synonymous_variant | 26/28 | 1 | NM_005336.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000152 AC: 38AN: 250630Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135626
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GnomAD4 exome AF: 0.000406 AC: 593AN: 1461042Hom.: 1 Cov.: 31 AF XY: 0.000406 AC XY: 295AN XY: 726688
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GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74336
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 09, 2018 | - - |
HDLBP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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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