chrX-153058284-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013364.6(PNMA3):c.1229G>A(p.Arg410His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000546 in 1,098,037 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013364.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNMA3 | NM_013364.6 | c.1229G>A | p.Arg410His | missense_variant | 2/2 | ENST00000593810.3 | |
PNMA3 | NM_001282535.2 | c.1229G>A | p.Arg410His | missense_variant | 2/3 | ||
PNMA3 | XR_938508.4 | n.1504G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNMA3 | ENST00000593810.3 | c.1229G>A | p.Arg410His | missense_variant | 2/2 | NM_013364.6 | P1 | ||
PNMA3 | ENST00000619635.1 | c.1229G>A | p.Arg410His | missense_variant | 2/3 | 1 | |||
PNMA3 | ENST00000424805.1 | c.1229G>A | p.Arg410His | missense_variant, NMD_transcript_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183155Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67771
GnomAD4 exome AF: 0.00000546 AC: 6AN: 1098037Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363397
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.1229G>A (p.R410H) alteration is located in exon 2 (coding exon 1) of the PNMA3 gene. This alteration results from a G to A substitution at nucleotide position 1229, causing the arginine (R) at amino acid position 410 to be replaced by a histidine (H). 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