chr4-122922773-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000339154.6(NUDT6):c.-270+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 586,484 control chromosomes in the GnomAD database, including 607 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.043 ( 462 hom., cov: 32)
Exomes 𝑓: 0.0059 ( 145 hom. )
Consequence
NUDT6
ENST00000339154.6 intron
ENST00000339154.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.595
Genes affected
NUDT6 (HGNC:8053): (nudix hydrolase 6) This gene overlaps and lies on the opposite strand from FGF2 gene, and is thought to be the FGF2 antisense gene. The two genes are independently transcribed, and their expression shows an inverse relationship, suggesting that this antisense transcript may regulate FGF2 expression. This gene has also been shown to have hormone-regulatory and antiproliferative actions in the pituitary that are independent of FGF2 expression. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 4-122922773-G-A is Benign according to our data. Variant chr4-122922773-G-A is described in ClinVar as [Benign]. Clinvar id is 1223283.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT6 | NM_198041.3 | c.-270+28C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT6 | ENST00000339154.6 | c.-270+28C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0430 AC: 6538AN: 152080Hom.: 465 Cov.: 32
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GnomAD4 exome AF: 0.00588 AC: 2553AN: 434286Hom.: 145 Cov.: 5 AF XY: 0.00499 AC XY: 1131AN XY: 226870
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GnomAD4 genome AF: 0.0430 AC: 6546AN: 152198Hom.: 462 Cov.: 32 AF XY: 0.0410 AC XY: 3047AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at