chr22-41844793-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004599.4(SREBF2):c.88+11435C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,912 control chromosomes in the GnomAD database, including 41,808 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 0.74 ( 41808 hom., cov: 30)
Consequence
SREBF2
NM_004599.4 intron
NM_004599.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.303
Publications
6 publications found
Genes affected
SREBF2 (HGNC:11290): (sterol regulatory element binding transcription factor 2) This gene encodes a member of the a ubiquitously expressed transcription factor that controls cholesterol homeostasis by regulating transcription of sterol-regulated genes. The encoded protein contains a basic helix-loop-helix-leucine zipper (bHLH-Zip) domain and binds the sterol regulatory element 1 motif. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
SREBF2 Gene-Disease associations (from GenCC):
- multiple congenital anomalies/dysmorphic syndromeInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- hereditary spastic paraplegiaInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SREBF2 | NM_004599.4 | c.88+11435C>T | intron_variant | Intron 1 of 18 | ENST00000361204.9 | NP_004590.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SREBF2 | ENST00000361204.9 | c.88+11435C>T | intron_variant | Intron 1 of 18 | 1 | NM_004599.4 | ENSP00000354476.4 | |||
SREBF2 | ENST00000424354.5 | n.88+11435C>T | intron_variant | Intron 1 of 21 | 1 | ENSP00000395728.1 | ||||
SREBF2 | ENST00000710853.1 | c.-3+10766C>T | intron_variant | Intron 1 of 18 | ENSP00000518526.1 |
Frequencies
GnomAD3 genomes AF: 0.737 AC: 111937AN: 151794Hom.: 41743 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
111937
AN:
151794
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.738 AC: 112065AN: 151912Hom.: 41808 Cov.: 30 AF XY: 0.738 AC XY: 54787AN XY: 74246 show subpopulations
GnomAD4 genome
AF:
AC:
112065
AN:
151912
Hom.:
Cov.:
30
AF XY:
AC XY:
54787
AN XY:
74246
show subpopulations
African (AFR)
AF:
AC:
33774
AN:
41426
American (AMR)
AF:
AC:
12384
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
2444
AN:
3468
East Asian (EAS)
AF:
AC:
2664
AN:
5142
South Asian (SAS)
AF:
AC:
3670
AN:
4810
European-Finnish (FIN)
AF:
AC:
7171
AN:
10544
Middle Eastern (MID)
AF:
AC:
212
AN:
294
European-Non Finnish (NFE)
AF:
AC:
47464
AN:
67936
Other (OTH)
AF:
AC:
1582
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1447
2894
4340
5787
7234
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
842
1684
2526
3368
4210
<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:
2444
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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