chrX-115622258-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_005032.7(PLS3):āc.86A>Gā(p.Asn29Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000326 in 1,197,593 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. N29N) has been classified as Benign.
Frequency
Consequence
NM_005032.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLS3 | NM_005032.7 | c.86A>G | p.Asn29Ser | missense_variant | 3/16 | ENST00000355899.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS3 | ENST00000355899.8 | c.86A>G | p.Asn29Ser | missense_variant | 3/16 | 1 | NM_005032.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000215 AC: 24AN: 111782Hom.: 0 Cov.: 23 AF XY: 0.000177 AC XY: 6AN XY: 33942
GnomAD3 exomes AF: 0.0000353 AC: 6AN: 169880Hom.: 0 AF XY: 0.0000355 AC XY: 2AN XY: 56304
GnomAD4 exome AF: 0.0000138 AC: 15AN: 1085811Hom.: 0 Cov.: 26 AF XY: 0.00000283 AC XY: 1AN XY: 353001
GnomAD4 genome AF: 0.000215 AC: 24AN: 111782Hom.: 0 Cov.: 23 AF XY: 0.000177 AC XY: 6AN XY: 33942
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.86A>G (p.N29S) alteration is located in exon 3 (coding exon 2) of the PLS3 gene. This alteration results from a A to G substitution at nucleotide position 86, causing the asparagine (N) at amino acid position 29 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at