chr16-67662607-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001037281.2(PARD6A):c.998G>A(p.Gly333Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000418 in 1,604,676 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_001037281.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARD6A | NM_001037281.2 | c.998G>A | p.Gly333Glu | missense_variant | 3/3 | ENST00000458121.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARD6A | ENST00000458121.7 | c.998G>A | p.Gly333Glu | missense_variant | 3/3 | 1 | NM_001037281.2 | A1 | |
PARD6A | ENST00000219255.3 | c.1001G>A | p.Gly334Glu | missense_variant | 3/3 | 1 | P4 | ||
PARD6A | ENST00000602551.5 | c.911G>A | p.Gly304Glu | missense_variant | 3/3 | 5 | |||
PARD6A | ENST00000602727.1 | n.1158G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000208 AC: 5AN: 239904Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 130938
GnomAD4 exome AF: 0.0000448 AC: 65AN: 1452450Hom.: 0 Cov.: 32 AF XY: 0.0000429 AC XY: 31AN XY: 721842
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2022 | The c.1001G>A (p.G334E) alteration is located in exon 3 (coding exon 3) of the PARD6A gene. This alteration results from a G to A substitution at nucleotide position 1001, causing the glycine (G) at amino acid position 334 to be replaced by a glutamic acid (E). 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