2-205119027-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001302769.2(PARD3B):c.787G>A(p.Val263Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000517 in 1,606,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001302769.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARD3B | NM_001302769.2 | c.787G>A | p.Val263Ile | missense_variant | 7/23 | ENST00000406610.7 | NP_001289698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARD3B | ENST00000406610.7 | c.787G>A | p.Val263Ile | missense_variant | 7/23 | 1 | NM_001302769.2 | ENSP00000385848 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000744 AC: 18AN: 241940Hom.: 1 AF XY: 0.0000914 AC XY: 12AN XY: 131224
GnomAD4 exome AF: 0.0000543 AC: 79AN: 1453982Hom.: 0 Cov.: 30 AF XY: 0.0000636 AC XY: 46AN XY: 723114
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.787G>A (p.V263I) alteration is located in exon 7 (coding exon 7) of the PARD3B gene. This alteration results from a G to A substitution at nucleotide position 787, causing the valine (V) at amino acid position 263 to be replaced by an isoleucine (I). 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