chr12-53327732-TAAG-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001173467.3(SP7):c.*411_*413del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 191,964 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 0 hom. )
Consequence
SP7
NM_001173467.3 3_prime_UTR
NM_001173467.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0510
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SP7 | NM_001173467.3 | c.*411_*413del | 3_prime_UTR_variant | 3/3 | ENST00000536324.4 | ||
SP7 | NM_001300837.2 | c.*411_*413del | 3_prime_UTR_variant | 3/3 | |||
SP7 | NM_152860.2 | c.*411_*413del | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SP7 | ENST00000536324.4 | c.*411_*413del | 3_prime_UTR_variant | 3/3 | 2 | NM_001173467.3 | P1 | ||
SP7 | ENST00000303846.3 | c.*411_*413del | 3_prime_UTR_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00369 AC: 562AN: 152152Hom.: 3 Cov.: 32
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GnomAD4 exome AF: 0.000630 AC: 25AN: 39694Hom.: 0 AF XY: 0.000592 AC XY: 12AN XY: 20260
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GnomAD4 genome AF: 0.00369 AC: 562AN: 152270Hom.: 3 Cov.: 32 AF XY: 0.00341 AC XY: 254AN XY: 74450
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Osteogenesis Imperfecta, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at