Variant 2-241233832-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_005336.6(HDLBP):c.3276C>T(p.Asp1092Asp) 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 (no stars).

Frequency

Genomes: 𝑓 0.11 ( 3215 hom., cov: 32)

Exomes 𝑓: 0.013 ( 2947 hom. )

Consequence

HDLBP
NM_005336.6 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

HDLBP links:

ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]

ANO7 links:

HDLBP (HGNC:):

HDLBP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.616 with no splicing effect.

BA1

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	Protein	UniProt
HDLBP	NM_005336.6 linkuse as main transcript	c.3276C>T	p.Asp1092Asp	synonymous_variant	24/28	ENST00000310931.10	NP_005327.1	Q00341A0A024R4E5B2R5V9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931.10 linkuse as main transcript	c.3276C>T	p.Asp1092Asp	synonymous_variant	24/28	1	NM_005336.6	ENSP00000312042.4		A0A024R4E5

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17138

AN:

152062

Hom.:

3207

Cov.:

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.:

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

AF:

0.113

AC:

17181

AN:

152180

Hom.:

3215

Cov.:

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:

AN:

3476

EpiCase

AF:

0.00393

EpiControl

AF:

0.00273

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

HDLBP-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 11, 2019

This 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over