rs2289795

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005336.6(HDLBP):​c.2749+499T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,428 control chromosomes in the GnomAD database, including 6,153 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 0.27 ( 6141 hom., cov: 33)
Exomes 𝑓: 0.30 ( 12 hom. )

Consequence

HDLBP
NM_005336.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.693
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]

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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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HDLBPNM_005336.6 linkuse as main transcriptc.2749+499T>G intron_variant ENST00000310931.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HDLBPENST00000310931.10 linkuse as main transcriptc.2749+499T>G intron_variant 1 NM_005336.6 P1

Frequencies

GnomAD3 genomes
AF:
0.267
AC:
40638
AN:
152094
Hom.:
6140
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.184
Gnomad AMI
AF:
0.194
Gnomad AMR
AF:
0.192
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.635
Gnomad SAS
AF:
0.373
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.280
Gnomad OTH
AF:
0.261
GnomAD4 exome
AF:
0.301
AC:
65
AN:
216
Hom.:
12
AF XY:
0.295
AC XY:
33
AN XY:
112
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.750
Gnomad4 FIN exome
AF:
0.300
Gnomad4 NFE exome
AF:
0.289
Gnomad4 OTH exome
AF:
0.375
GnomAD4 genome
AF:
0.267
AC:
40667
AN:
152212
Hom.:
6141
Cov.:
33
AF XY:
0.276
AC XY:
20543
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.184
Gnomad4 AMR
AF:
0.192
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.635
Gnomad4 SAS
AF:
0.374
Gnomad4 FIN
AF:
0.399
Gnomad4 NFE
AF:
0.280
Gnomad4 OTH
AF:
0.262
Alfa
AF:
0.275
Hom.:
9950
Bravo
AF:
0.249
Asia WGS
AF:
0.464
AC:
1615
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.25
DANN
Benign
0.51
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs2289795; hg19: chr2-242177565; API