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2-241233832-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005336.6(HDLBP):c.3276C>T(p.Asp1092=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 1,614,026 control chromosomes in the GnomAD database, including 6,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 3215 hom., cov: 32)
Exomes 𝑓: 0.013 ( 2947 hom. )

Consequence

HDLBP
NM_005336.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.616
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-241233832-G-A is Benign according to our data. Variant chr2-241233832-G-A is described in ClinVar as [Benign]. Clinvar id is 3057037.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.616 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HDLBPNM_005336.6 linkuse as main transcriptc.3276C>T p.Asp1092= synonymous_variant 24/28 ENST00000310931.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HDLBPENST00000310931.10 linkuse as main transcriptc.3276C>T p.Asp1092= synonymous_variant 24/281 NM_005336.6 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
17138
AN:
152062
Hom.:
3207
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0429
Gnomad ASJ
AF:
0.0239
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0110
Gnomad FIN
AF:
0.000189
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00231
Gnomad OTH
AF:
0.0789
GnomAD3 exomes
AF:
0.0323
AC:
8135
AN:
251474
Hom.:
1314
AF XY:
0.0247
AC XY:
3354
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.395
Gnomad AMR exome
AF:
0.0208
Gnomad ASJ exome
AF:
0.0255
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0127
Gnomad FIN exome
AF:
0.000185
Gnomad NFE exome
AF:
0.00201
Gnomad OTH exome
AF:
0.0181
GnomAD4 exome
AF:
0.0135
AC:
19699
AN:
1461846
Hom.:
2947
Cov.:
31
AF XY:
0.0123
AC XY:
8909
AN XY:
727224
show subpopulations
Gnomad4 AFR exome
AF:
0.403
Gnomad4 AMR exome
AF:
0.0242
Gnomad4 ASJ exome
AF:
0.0267
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0123
Gnomad4 FIN exome
AF:
0.000281
Gnomad4 NFE exome
AF:
0.00126
Gnomad4 OTH exome
AF:
0.0294
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.113
AC:
17181
AN:
152180
Hom.:
3215
Cov.:
32
AF XY:
0.109
AC XY:
8079
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.0428
Gnomad4 ASJ
AF:
0.0239
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0106
Gnomad4 FIN
AF:
0.000189
Gnomad4 NFE
AF:
0.00231
Gnomad4 OTH
AF:
0.0781
Alfa
AF:
0.0494
Hom.:
626
Bravo
AF:
0.130
Asia WGS
AF:
0.0260
AC:
92
AN:
3476
EpiCase
AF:
0.00393
EpiControl
AF:
0.00273

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

HDLBP-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 11, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.099
Dann
Benign
0.41
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2230359; hg19: chr2-242173247; API