chr9-86337398-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_024617.4(TUT7):c.1455+21T>G variant causes a intron change. The variant allele was found at a frequency of 0.0315 in 1,596,050 control chromosomes in the GnomAD database, including 955 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 0.024 ( 73 hom., cov: 32)
Exomes 𝑓: 0.032 ( 882 hom. )
Consequence
TUT7
NM_024617.4 intron
NM_024617.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.89
Genes affected
TUT7 (HGNC:25817): (terminal uridylyl transferase 7) Enables RNA uridylyltransferase activity and miRNA binding activity. Involved in RNA metabolic process and negative regulation of transposition, RNA-mediated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.79).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0244 (3722/152304) while in subpopulation NFE AF= 0.0381 (2594/68026). AF 95% confidence interval is 0.0369. There are 73 homozygotes in gnomad4. There are 1786 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 73 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUT7 | NM_024617.4 | c.1455+21T>G | intron_variant | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.1455+21T>G | intron_variant | 5 | NM_024617.4 | P1 | |||
TUT7 | ENST00000375960.6 | c.1086+5677T>G | intron_variant | 1 | |||||
TUT7 | ENST00000375948.2 | c.*15T>G | 3_prime_UTR_variant | 5/5 | 2 | ||||
TUT7 | ENST00000277141.10 | c.-800+21T>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0245 AC: 3722AN: 152186Hom.: 73 Cov.: 32
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GnomAD3 exomes AF: 0.0255 AC: 5863AN: 230060Hom.: 114 AF XY: 0.0260 AC XY: 3239AN XY: 124602
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GnomAD4 exome AF: 0.0322 AC: 46482AN: 1443746Hom.: 882 Cov.: 30 AF XY: 0.0317 AC XY: 22772AN XY: 718092
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GnomAD4 genome ? AF: 0.0244 AC: 3722AN: 152304Hom.: 73 Cov.: 32 AF XY: 0.0240 AC XY: 1786AN XY: 74480
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at