rs2228013
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_006167.4(NKX3-1):c.154C>T(p.Arg52Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 1,580,730 control chromosomes in the GnomAD database, including 1,467 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX3-1 | NM_006167.4 | c.154C>T | p.Arg52Cys | missense_variant | 1/2 | ENST00000380871.5 | |
LOC107986930 | XR_001745842.2 | n.1312+13986G>A | intron_variant, non_coding_transcript_variant | ||||
NKX3-1 | NM_001256339.1 | c.34-105C>T | intron_variant | ||||
NKX3-1 | NR_046072.2 | n.35+168C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX3-1 | ENST00000380871.5 | c.154C>T | p.Arg52Cys | missense_variant | 1/2 | 1 | NM_006167.4 | P2 | |
NKX3-1 | ENST00000523261.1 | c.34-105C>T | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0321 AC: 4890AN: 152114Hom.: 105 Cov.: 33
GnomAD3 exomes AF: 0.0344 AC: 6942AN: 202040Hom.: 151 AF XY: 0.0355 AC XY: 4028AN XY: 113310
GnomAD4 exome AF: 0.0428 AC: 61086AN: 1428508Hom.: 1362 Cov.: 31 AF XY: 0.0427 AC XY: 30330AN XY: 710898
GnomAD4 genome ? AF: 0.0321 AC: 4888AN: 152222Hom.: 105 Cov.: 33 AF XY: 0.0305 AC XY: 2271AN XY: 74422
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at