8-23682699-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.191G>T(p.Gly64Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000632 in 1,581,574 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.191G>T | p.Gly64Val | missense_variant | 1/2 | ENST00000380871.5 | |
LOC107986930 | XR_001745842.2 | n.1312+13949C>A | intron_variant, non_coding_transcript_variant | ||||
NKX3-1 | NM_001256339.1 | c.34-68G>T | intron_variant | ||||
NKX3-1 | NR_046072.2 | n.35+205G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.191G>T | p.Gly64Val | missense_variant | 1/2 | 1 | NM_006167.4 | P2 | |
NKX3-1 | ENST00000523261.1 | c.34-68G>T | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000972 AC: 2AN: 205666Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 115176
GnomAD4 exome AF: 0.00000560 AC: 8AN: 1429420Hom.: 0 Cov.: 30 AF XY: 0.00000562 AC XY: 4AN XY: 711390
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.191G>T (p.G64V) 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 191, causing the glycine (G) at amino acid position 64 to be replaced by a valine (V). 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