chr8-23681332-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006167.4(NKX3-1):c.594G>A(p.Pro198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000492 in 1,614,174 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0026 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00027 ( 2 hom. )
Consequence
NKX3-1
NM_006167.4 synonymous
NM_006167.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.14
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 8-23681332-C-T is Benign according to our data. Variant chr8-23681332-C-T is described in ClinVar as [Benign]. Clinvar id is 721025.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX3-1 | NM_006167.4 | c.594G>A | p.Pro198= | synonymous_variant | 2/2 | ENST00000380871.5 | |
LOC107986930 | XR_001745842.2 | n.1312+12582C>T | intron_variant, non_coding_transcript_variant | ||||
NKX3-1 | NM_001256339.1 | c.369G>A | p.Pro123= | synonymous_variant | 3/3 | ||
NKX3-1 | NR_046072.2 | n.36-190G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.594G>A | p.Pro198= | synonymous_variant | 2/2 | 1 | NM_006167.4 | P2 | |
NKX3-1 | ENST00000523261.1 | c.369G>A | p.Pro123= | synonymous_variant | 3/3 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00264 AC: 401AN: 152170Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000624 AC: 157AN: 251460Hom.: 1 AF XY: 0.000471 AC XY: 64AN XY: 135898
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GnomAD4 exome AF: 0.000270 AC: 394AN: 1461886Hom.: 2 Cov.: 31 AF XY: 0.000241 AC XY: 175AN XY: 727246
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GnomAD4 genome AF: 0.00263 AC: 400AN: 152288Hom.: 2 Cov.: 33 AF XY: 0.00266 AC XY: 198AN XY: 74458
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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 | Invitae | Jan 08, 2018 | - - |
Computational 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