chr11-112169304-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_031275.4(TEX12):āc.36A>Gā(p.Arg12Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,611,342 control chromosomes in the GnomAD database, including 50,407 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: š 0.21 ( 3810 hom., cov: 32)
Exomes š: 0.25 ( 46597 hom. )
Consequence
TEX12
NM_031275.4 synonymous
NM_031275.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.47
Genes affected
TEX12 (HGNC:11734): (testis expressed 12) This gene is similar to a mouse gene that is expressed in the testis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP7
Synonymous conserved (PhyloP=1.47 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX12 | NM_031275.4 | c.36A>G | p.Arg12Arg | synonymous_variant | 2/5 | ENST00000280358.5 | NP_112565.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX12 | ENST00000280358.5 | c.36A>G | p.Arg12Arg | synonymous_variant | 2/5 | 1 | NM_031275.4 | ENSP00000280358.4 | ||
ENSG00000255292 | ENST00000532699.1 | n.315-1115A>G | intron_variant | 3 | ENSP00000456434.1 |
Frequencies
GnomAD3 genomes AF: 0.207 AC: 31419AN: 152038Hom.: 3809 Cov.: 32
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GnomAD3 exomes AF: 0.242 AC: 60892AN: 251194Hom.: 7872 AF XY: 0.244 AC XY: 33132AN XY: 135778
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GnomAD4 exome AF: 0.250 AC: 364210AN: 1459186Hom.: 46597 Cov.: 31 AF XY: 0.250 AC XY: 181215AN XY: 725998
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GnomAD4 genome AF: 0.206 AC: 31410AN: 152156Hom.: 3810 Cov.: 32 AF XY: 0.209 AC XY: 15518AN XY: 74382
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at