rs9898876
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000575314.5(SHBG):c.-61-6774G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,106 control chromosomes in the GnomAD database, including 2,406 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 0.18 ( 2406 hom., cov: 32)
Consequence
SHBG
ENST00000575314.5 intron
ENST00000575314.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.884
Publications
20 publications found
Genes affected
SHBG (HGNC:10839): (sex hormone binding globulin) This gene encodes a steroid binding protein that was first described as a plasma protein secreted by the liver but is now thought to participate in the regulation of steroid responses. The encoded protein transports androgens and estrogens in the blood, binding each steroid molecule as a dimer formed from identical or nearly identical monomers. Polymorphisms in this gene have been associated with polycystic ovary syndrome and type 2 diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHBG | ENST00000575314.5 | c.-61-6774G>T | intron_variant | Intron 1 of 7 | 1 | ENSP00000458559.1 | ||||
SHBG | ENST00000572262.5 | c.-61-6774G>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000459999.1 | ||||
SHBG | ENST00000574539.5 | c.-61-6774G>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000458181.1 |
Frequencies
GnomAD3 genomes AF: 0.176 AC: 26718AN: 151988Hom.: 2397 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
26718
AN:
151988
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.176 AC: 26737AN: 152106Hom.: 2406 Cov.: 32 AF XY: 0.171 AC XY: 12710AN XY: 74362 show subpopulations
GnomAD4 genome
AF:
AC:
26737
AN:
152106
Hom.:
Cov.:
32
AF XY:
AC XY:
12710
AN XY:
74362
show subpopulations
African (AFR)
AF:
AC:
7889
AN:
41466
American (AMR)
AF:
AC:
2083
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
729
AN:
3468
East Asian (EAS)
AF:
AC:
816
AN:
5168
South Asian (SAS)
AF:
AC:
784
AN:
4830
European-Finnish (FIN)
AF:
AC:
1167
AN:
10602
Middle Eastern (MID)
AF:
AC:
20
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12752
AN:
67988
Other (OTH)
AF:
AC:
349
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1158
2317
3475
4634
5792
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
290
580
870
1160
1450
<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:
621
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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