rs3813637
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032126.5(TEX35):c.*105C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,328,354 control chromosomes in the GnomAD database, including 9,117 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 ( 1694 hom., cov: 33)
Exomes 𝑓: 0.11 ( 7423 hom. )
Consequence
TEX35
NM_032126.5 3_prime_UTR
NM_032126.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.237
Genes affected
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX35 | NM_032126.5 | c.*105C>G | 3_prime_UTR_variant | 9/9 | ENST00000319416.7 | ||
TEX35 | NM_001170722.2 | c.611-757C>G | intron_variant | ||||
TEX35 | NM_001170724.2 | c.587-757C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX35 | ENST00000319416.7 | c.*105C>G | 3_prime_UTR_variant | 9/9 | 1 | NM_032126.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.132 AC: 20067AN: 152070Hom.: 1681 Cov.: 33
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GnomAD4 exome AF: 0.108 AC: 126854AN: 1176166Hom.: 7423 Cov.: 29 AF XY: 0.107 AC XY: 60199AN XY: 563714
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GnomAD4 genome ? AF: 0.132 AC: 20119AN: 152188Hom.: 1694 Cov.: 33 AF XY: 0.126 AC XY: 9380AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at