chr18-80160580-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032510.4(PARD6G):c.322G>T(p.Ala108Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,456,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032510.4 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 |
---|---|---|---|---|---|---|---|
PARD6G | NM_032510.4 | c.322G>T | p.Ala108Ser | missense_variant | 3/3 | ENST00000353265.8 | |
PARD6G-AS1 | NR_028340.1 | n.331+12326C>A | intron_variant, non_coding_transcript_variant | ||||
PARD6G-AS1 | NR_028339.1 | n.332-1936C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARD6G | ENST00000353265.8 | c.322G>T | p.Ala108Ser | missense_variant | 3/3 | 1 | NM_032510.4 | P1 | |
PARD6G-AS1 | ENST00000662611.1 | n.176-1936C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000285 AC: 2AN: 70246Hom.: 0 AF XY: 0.0000275 AC XY: 1AN XY: 36422
GnomAD4 exome AF: 0.0000153 AC: 20AN: 1304722Hom.: 0 Cov.: 31 AF XY: 0.0000126 AC XY: 8AN XY: 635268
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.322G>T (p.A108S) alteration is located in exon 3 (coding exon 3) of the PARD6G gene. This alteration results from a G to T substitution at nucleotide position 322, causing the alanine (A) at amino acid position 108 to be replaced by a serine (S). 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