8-23681020-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006167.4(NKX3-1):c.*201T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 476,546 control chromosomes in the GnomAD database, including 99,559 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 0.62 ( 29608 hom., cov: 32)
Exomes 𝑓: 0.65 ( 69951 hom. )
Consequence
NKX3-1
NM_006167.4 3_prime_UTR
NM_006167.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0210
Genes affected
NKX3-1 (HGNC:7838): (NK3 homeobox 1) This gene encodes a homeobox-containing transcription factor. This transcription factor functions as a negative regulator of epithelial cell growth in prostate tissue. Aberrant expression of this gene is associated with prostate tumor progression. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jan 2012]
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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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NKX3-1 | NM_006167.4 | c.*201T>C | 3_prime_UTR_variant | 2/2 | ENST00000380871.5 | NP_006158.2 | ||
NKX3-1 | NM_001256339.1 | c.*201T>C | 3_prime_UTR_variant | 3/3 | NP_001243268.1 | |||
NKX3-1 | NR_046072.2 | n.158T>C | non_coding_transcript_exon_variant | 2/2 | ||||
LOC107986930 | XR_001745842.2 | n.1312+12270A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.*201T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_006167.4 | ENSP00000370253.4 | |||
NKX3-1 | ENST00000523261.1 | c.*201T>C | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000429729.1 |
Frequencies
GnomAD3 genomes AF: 0.619 AC: 94087AN: 151994Hom.: 29597 Cov.: 32
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GnomAD4 exome AF: 0.653 AC: 211848AN: 324434Hom.: 69951 Cov.: 4 AF XY: 0.653 AC XY: 108221AN XY: 165840
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GnomAD4 genome AF: 0.619 AC: 94141AN: 152112Hom.: 29608 Cov.: 32 AF XY: 0.613 AC XY: 45592AN XY: 74348
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at