chr8-23682768-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.122G>T(p.Arg41Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000482 in 1,575,206 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.122G>T | p.Arg41Leu | missense_variant | 1/2 | ENST00000380871.5 | |
LOC107986930 | XR_001745842.2 | n.1312+14018C>A | intron_variant, non_coding_transcript_variant | ||||
NKX3-1 | NM_001256339.1 | c.33+89G>T | intron_variant | ||||
NKX3-1 | NR_046072.2 | n.35+136G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.122G>T | p.Arg41Leu | missense_variant | 1/2 | 1 | NM_006167.4 | P2 | |
NKX3-1 | ENST00000523261.1 | c.33+89G>T | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000100 AC: 19AN: 189538Hom.: 1 AF XY: 0.0000942 AC XY: 10AN XY: 106160
GnomAD4 exome AF: 0.0000527 AC: 75AN: 1423040Hom.: 0 Cov.: 31 AF XY: 0.0000608 AC XY: 43AN XY: 707376
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.122G>T (p.R41L) 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 122, causing the arginine (R) at amino acid position 41 to be replaced by a leucine (L). 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