chr7-120788552-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_012338.4(TSPAN12):c.*40T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000317 in 1,612,912 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 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00034 ( 0 hom. )
Consequence
TSPAN12
NM_012338.4 3_prime_UTR
NM_012338.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.531
Genes affected
TSPAN12 (HGNC:21641): (tetraspanin 12) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 7-120788552-A-G is Benign according to our data. Variant chr7-120788552-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 358759.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000657 (10/152248) while in subpopulation NFE AF= 0.000147 (10/68052). AF 95% confidence interval is 0.0000791. There are 0 homozygotes in gnomad4. There are 4 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN12 | NM_012338.4 | c.*40T>C | 3_prime_UTR_variant | 8/8 | ENST00000222747.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN12 | ENST00000222747.8 | c.*40T>C | 3_prime_UTR_variant | 8/8 | 1 | NM_012338.4 | P1 | ||
TSPAN12 | ENST00000415871.5 | c.*40T>C | 3_prime_UTR_variant | 9/9 | 5 | P1 | |||
TSPAN12 | ENST00000450414.5 | c.*808T>C | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152248Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000600 AC: 15AN: 250092Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135148
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GnomAD4 exome AF: 0.000343 AC: 501AN: 1460664Hom.: 0 Cov.: 27 AF XY: 0.000312 AC XY: 227AN XY: 726724
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74380
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Exudative vitreoretinopathy 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at