chrX-153058211-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_013364.6(PNMA3):c.1156C>T(p.Arg386Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,210,671 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R386Q) has been classified as Likely benign.
Frequency
Consequence
NM_013364.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNMA3 | NM_013364.6 | c.1156C>T | p.Arg386Trp | missense_variant | 2/2 | ENST00000593810.3 | |
PNMA3 | NM_001282535.2 | c.1156C>T | p.Arg386Trp | missense_variant | 2/3 | ||
PNMA3 | XR_938508.4 | n.1431C>T | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNMA3 | ENST00000593810.3 | c.1156C>T | p.Arg386Trp | missense_variant | 2/2 | NM_013364.6 | P1 | ||
PNMA3 | ENST00000619635.1 | c.1156C>T | p.Arg386Trp | missense_variant | 2/3 | 1 | |||
PNMA3 | ENST00000424805.1 | c.1156C>T | p.Arg386Trp | missense_variant, NMD_transcript_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000886 AC: 1AN: 112819Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34977
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181771Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66879
GnomAD4 exome AF: 0.0000164 AC: 18AN: 1097852Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 5AN XY: 363248
GnomAD4 genome ? AF: 0.00000886 AC: 1AN: 112819Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34977
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.1156C>T (p.R386W) alteration is located in exon 2 (coding exon 1) of the PNMA3 gene. This alteration results from a C to T substitution at nucleotide position 1156, causing the arginine (R) at amino acid position 386 to be replaced by a tryptophan (W). 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