NM_001173467.3:c.1146T>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001173467.3(SP7):c.1146T>C(p.Gly382Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SP7
NM_001173467.3 synonymous
NM_001173467.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.72
Publications
0 publications found
Genes affected
SP7 (HGNC:17321): (Sp7 transcription factor) This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein is a bone specific transcription factor and is required for osteoblast differentiation and bone formation.[provided by RefSeq, Jul 2010]
SP7 Gene-Disease associations (from GenCC):
- osteogenesis imperfecta type 12Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia
- osteogenesis imperfecta type 4Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant 12-53328296-A-G is Benign according to our data. Variant chr12-53328296-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2821249.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-5.72 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001173467.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SP7 | NM_001173467.3 | MANE Select | c.1146T>C | p.Gly382Gly | synonymous | Exon 3 of 3 | NP_001166938.1 | Q8TDD2-1 | |
| SP7 | NM_152860.2 | c.1146T>C | p.Gly382Gly | synonymous | Exon 2 of 2 | NP_690599.1 | Q8TDD2-1 | ||
| SP7 | NM_001300837.2 | c.1092T>C | p.Gly364Gly | synonymous | Exon 3 of 3 | NP_001287766.1 | Q8TDD2-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SP7 | ENST00000536324.4 | TSL:2 MANE Select | c.1146T>C | p.Gly382Gly | synonymous | Exon 3 of 3 | ENSP00000443827.2 | Q8TDD2-1 | |
| SP7 | ENST00000303846.3 | TSL:1 | c.1146T>C | p.Gly382Gly | synonymous | Exon 2 of 2 | ENSP00000302812.3 | Q8TDD2-1 | |
| SP7 | ENST00000537210.2 | TSL:1 | c.1092T>C | p.Gly364Gly | synonymous | Exon 2 of 2 | ENSP00000441367.2 | Q8TDD2-2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 150256Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
150256
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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Gnomad ASJ
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458062Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725032 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1458062
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
725032
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33428
American (AMR)
AF:
AC:
0
AN:
44448
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25844
East Asian (EAS)
AF:
AC:
0
AN:
39670
South Asian (SAS)
AF:
AC:
0
AN:
85724
European-Finnish (FIN)
AF:
AC:
0
AN:
53174
Middle Eastern (MID)
AF:
AC:
0
AN:
5748
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109840
Other (OTH)
AF:
AC:
1
AN:
60186
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00 AC: 0AN: 150256Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73330
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
150256
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
73330
African (AFR)
AF:
AC:
0
AN:
40784
American (AMR)
AF:
AC:
0
AN:
15084
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3452
East Asian (EAS)
AF:
AC:
0
AN:
5114
South Asian (SAS)
AF:
AC:
0
AN:
4606
European-Finnish (FIN)
AF:
AC:
0
AN:
10502
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67418
Other (OTH)
AF:
AC:
0
AN:
2068
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational 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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