NM_005505.5:c.*94G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005505.5(SCARB1):​c.*94G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,348,458 control chromosomes in the GnomAD database, including 1,264 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 789 hom., cov: 33)
Exomes 𝑓: 0.0051 ( 475 hom. )

Consequence

SCARB1
NM_005505.5 3_prime_UTR

Scores

14

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.743

Publications

9 publications found
Variant links:
Genes affected
SCARB1 (HGNC:1664): (scavenger receptor class B member 1) The protein encoded by this gene is a plasma membrane receptor for high density lipoprotein cholesterol (HDL). The encoded protein mediates cholesterol transfer to and from HDL. In addition, this protein is a receptor for hepatitis C virus glycoprotein E2 and facilitates cell entry by the virus, SARS-CoV2. [provided by RefSeq, Oct 2021]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0046088696).
BP6
Variant 12-124778493-C-T is Benign according to our data. Variant chr12-124778493-C-T is described in ClinVar as [Benign]. Clinvar id is 1297808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCARB1NM_005505.5 linkc.*94G>A 3_prime_UTR_variant Exon 13 of 13 ENST00000261693.11 NP_005496.4 Q8WTV0-2A0A024RBS4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCARB1ENST00000261693.11 linkc.*94G>A 3_prime_UTR_variant Exon 13 of 13 1 NM_005505.5 ENSP00000261693.6 Q8WTV0-2

Frequencies

GnomAD3 genomes
AF:
0.0539
AC:
8192
AN:
151954
Hom.:
785
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.187
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0198
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000416
Gnomad FIN
AF:
0.000189
Gnomad MID
AF:
0.0318
Gnomad NFE
AF:
0.00116
Gnomad OTH
AF:
0.0350
GnomAD2 exomes
AF:
0.0140
AC:
424
AN:
30328
AF XY:
0.0113
show subpopulations
Gnomad AFR exome
AF:
0.198
Gnomad AMR exome
AF:
0.0171
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000108
Gnomad NFE exome
AF:
0.000909
Gnomad OTH exome
AF:
0.00797
GnomAD4 exome
AF:
0.00510
AC:
6101
AN:
1196384
Hom.:
475
Cov.:
32
AF XY:
0.00450
AC XY:
2596
AN XY:
576648
show subpopulations
African (AFR)
AF:
0.194
AC:
4668
AN:
24036
American (AMR)
AF:
0.0176
AC:
168
AN:
9568
Ashkenazi Jewish (ASJ)
AF:
0.000424
AC:
7
AN:
16506
East Asian (EAS)
AF:
0.0000360
AC:
1
AN:
27788
South Asian (SAS)
AF:
0.000343
AC:
15
AN:
43736
European-Finnish (FIN)
AF:
0.0000957
AC:
4
AN:
41802
Middle Eastern (MID)
AF:
0.00957
AC:
41
AN:
4286
European-Non Finnish (NFE)
AF:
0.000602
AC:
590
AN:
979938
Other (OTH)
AF:
0.0125
AC:
607
AN:
48724
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.479
Heterozygous variant carriers
0
268
537
805
1074
1342
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
170
340
510
680
850
<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:
0.0541
AC:
8227
AN:
152074
Hom.:
789
Cov.:
33
AF XY:
0.0525
AC XY:
3906
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.187
AC:
7759
AN:
41438
American (AMR)
AF:
0.0197
AC:
302
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5186
South Asian (SAS)
AF:
0.000416
AC:
2
AN:
4808
European-Finnish (FIN)
AF:
0.000189
AC:
2
AN:
10602
Middle Eastern (MID)
AF:
0.0342
AC:
10
AN:
292
European-Non Finnish (NFE)
AF:
0.00116
AC:
79
AN:
67968
Other (OTH)
AF:
0.0347
AC:
73
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
335
670
1004
1339
1674
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
82
164
246
328
410
<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:
0.0355
Hom.:
100
Bravo
AF:
0.0624
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.158
AC:
644
ESP6500EA
AF:
0.00193
AC:
16
ExAC
AF:
0.0112
AC:
1227
Asia WGS
AF:
0.00837
AC:
29
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Apr 01, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 27651445) -

-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.66
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
1.7
DANN
Benign
0.96
Eigen
Benign
-0.84
Eigen_PC
Benign
-0.93
FATHMM_MKL
Benign
0.046
N
LIST_S2
Benign
0.42
T
MetaRNN
Benign
0.0046
T
MetaSVM
Benign
-1.1
T
PhyloP100
-0.74
PROVEAN
Benign
-0.51
N
REVEL
Benign
0.022
Sift
Benign
0.060
T
Sift4G
Benign
0.21
T
Vest4
0.060
MutPred
0.19
Gain of glycosylation at P497 (P = 0.071);
ClinPred
0.00078
T
GERP RS
1.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Mutation Taster
=99/1
polymorphism (auto)

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

Other links and lift over

dbSNP: rs701103; hg19: chr12-125263039; COSMIC: COSV55550572; COSMIC: COSV55550572; API