8-23682713-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006167.4(NKX3-1):c.177G>T(p.Glu59Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000145 in 1,583,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX3-1 | NM_006167.4 | c.177G>T | p.Glu59Asp | missense_variant | 1/2 | ENST00000380871.5 | |
LOC107986930 | XR_001745842.2 | n.1312+13963C>A | intron_variant, non_coding_transcript_variant | ||||
NKX3-1 | NM_001256339.1 | c.34-82G>T | intron_variant | ||||
NKX3-1 | NR_046072.2 | n.35+191G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.177G>T | p.Glu59Asp | missense_variant | 1/2 | 1 | NM_006167.4 | P2 | |
NKX3-1 | ENST00000523261.1 | c.34-82G>T | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000140 AC: 20AN: 1431110Hom.: 0 Cov.: 30 AF XY: 0.00000842 AC XY: 6AN XY: 712318
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2023 | The c.177G>T (p.E59D) alteration is located in exon 1 (coding exon 1) of the NKX3-1 gene. This alteration results from a G to T substitution at nucleotide position 177, causing the glutamic acid (E) at amino acid position 59 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at