4-13542053-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001189.4(NKX3-2):c.942G>A(p.Pro314Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,454,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001189.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NKX3-2 | NM_001189.4 | c.942G>A | p.Pro314Pro | synonymous_variant | Exon 2 of 2 | ENST00000382438.6 | NP_001180.1 | |
NKX3-2 | XM_047416049.1 | c.942G>A | p.Pro314Pro | synonymous_variant | Exon 3 of 3 | XP_047272005.1 | ||
NKX3-2 | XM_047416050.1 | c.942G>A | p.Pro314Pro | synonymous_variant | Exon 3 of 3 | XP_047272006.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454142Hom.: 0 Cov.: 31 AF XY: 0.00000277 AC XY: 2AN XY: 722734
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at