chr12-53328138-C-CA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001173467.3(SP7):c.*7dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,602,194 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001173467.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SP7 | NM_001173467.3 | c.*7dupT | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000536324.4 | NP_001166938.1 | ||
SP7 | NM_152860.2 | c.*7dupT | 3_prime_UTR_variant | Exon 2 of 2 | NP_690599.1 | |||
SP7 | NM_001300837.2 | c.*7dupT | 3_prime_UTR_variant | Exon 3 of 3 | NP_001287766.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SP7 | ENST00000536324 | c.*7dupT | 3_prime_UTR_variant | Exon 3 of 3 | 2 | NM_001173467.3 | ENSP00000443827.2 | |||
SP7 | ENST00000303846 | c.*7dupT | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000302812.3 | ||||
SP7 | ENST00000537210.2 | c.*7dupT | downstream_gene_variant | 1 | ENSP00000441367.2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 11AN: 228918Hom.: 0 AF XY: 0.0000558 AC XY: 7AN XY: 125356
GnomAD4 exome AF: 0.000148 AC: 215AN: 1450064Hom.: 0 Cov.: 29 AF XY: 0.000150 AC XY: 108AN XY: 720664
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: SP7 c.*7dupT is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 4.8e-05 in 228918 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in SP7 causing Osteogenesis Imperfecta Type 12, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.*7dupT in individuals affected with Osteogenesis Imperfecta Type 12 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at