NM_005336.6:c.-102-4716T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
Publications
13 publications found
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 was made for transcript
Our verdict: Benign. The variant received -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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDLBP | NM_005336.6 | c.-102-4716T>C | intron_variant | Intron 1 of 27 | ENST00000310931.10 | NP_005327.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDLBP | ENST00000310931.10 | c.-102-4716T>C | intron_variant | Intron 1 of 27 | 1 | NM_005336.6 | ENSP00000312042.4 |
Frequencies
GnomAD3 genomes AF: 0.522 AC: 79340AN: 151868Hom.: 21553 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
79340
AN:
151868
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.558 AC: 464836AN: 832320Hom.: 130252 Cov.: 24 AF XY: 0.558 AC XY: 214308AN XY: 384408 show subpopulations
GnomAD4 exome
AF:
AC:
464836
AN:
832320
Hom.:
Cov.:
24
AF XY:
AC XY:
214308
AN XY:
384408
show subpopulations
African (AFR)
AF:
AC:
5989
AN:
15766
American (AMR)
AF:
AC:
678
AN:
984
Ashkenazi Jewish (ASJ)
AF:
AC:
2810
AN:
5152
East Asian (EAS)
AF:
AC:
2843
AN:
3628
South Asian (SAS)
AF:
AC:
10174
AN:
16440
European-Finnish (FIN)
AF:
AC:
180
AN:
280
Middle Eastern (MID)
AF:
AC:
885
AN:
1620
European-Non Finnish (NFE)
AF:
AC:
425801
AN:
761158
Other (OTH)
AF:
AC:
15476
AN:
27292
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
10712
21424
32136
42848
53560
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
16346
32692
49038
65384
81730
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.523 AC: 79437AN: 151986Hom.: 21600 Cov.: 30 AF XY: 0.526 AC XY: 39066AN XY: 74276 show subpopulations
GnomAD4 genome
AF:
AC:
79437
AN:
151986
Hom.:
Cov.:
30
AF XY:
AC XY:
39066
AN XY:
74276
show subpopulations
African (AFR)
AF:
AC:
16465
AN:
41458
American (AMR)
AF:
AC:
9878
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1891
AN:
3470
East Asian (EAS)
AF:
AC:
4016
AN:
5162
South Asian (SAS)
AF:
AC:
2990
AN:
4824
European-Finnish (FIN)
AF:
AC:
5537
AN:
10544
Middle Eastern (MID)
AF:
AC:
144
AN:
292
European-Non Finnish (NFE)
AF:
AC:
37074
AN:
67932
Other (OTH)
AF:
AC:
1181
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1861
3722
5583
7444
9305
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
708
1416
2124
2832
3540
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2548
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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