rs6802503
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004593.3(TRA2B):c.334-118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 803,310 control chromosomes in the GnomAD database, including 13,078 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: 𝑓 0.13 ( 1676 hom., cov: 32)
Exomes 𝑓: 0.18 ( 11402 hom. )
Consequence
TRA2B
NM_004593.3 intron
NM_004593.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.626
Genes affected
TRA2B (HGNC:10781): (transformer 2 beta homolog) This gene encodes a nuclear protein which functions as sequence-specific serine/arginine splicing factor which plays a role in mRNA processing, splicing patterns, and gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRA2B | NM_004593.3 | c.334-118T>G | intron_variant | ENST00000453386.7 | |||
TRA2B | NM_001243879.2 | c.34-118T>G | intron_variant | ||||
TRA2B | XM_047448717.1 | c.34-118T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRA2B | ENST00000453386.7 | c.334-118T>G | intron_variant | 1 | NM_004593.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19349AN: 152160Hom.: 1675 Cov.: 32
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GnomAD4 exome AF: 0.179 AC: 116345AN: 651032Hom.: 11402 Cov.: 9 AF XY: 0.177 AC XY: 58020AN XY: 328606
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GnomAD4 genome ? AF: 0.127 AC: 19344AN: 152278Hom.: 1676 Cov.: 32 AF XY: 0.121 AC XY: 9042AN XY: 74456
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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