rs11575948
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018916.4(PCDHGA3):c.460A>C(p.Ile154Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 1,613,822 control chromosomes in the GnomAD database, including 9,080 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_018916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDHGA3 | NM_018916.4 | c.460A>C | p.Ile154Leu | missense_variant | Exon 1 of 4 | ENST00000253812.8 | NP_061739.2 | |
PCDHGA2 | NM_018915.4 | c.2424+3098A>C | intron_variant | Intron 1 of 3 | ENST00000394576.3 | NP_061738.1 | ||
PCDHGA1 | NM_018912.3 | c.2421+11388A>C | intron_variant | Intron 1 of 3 | ENST00000517417.3 | NP_061735.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA3 | ENST00000253812.8 | c.460A>C | p.Ile154Leu | missense_variant | Exon 1 of 4 | 1 | NM_018916.4 | ENSP00000253812.7 | ||
PCDHGA2 | ENST00000394576.3 | c.2424+3098A>C | intron_variant | Intron 1 of 3 | 1 | NM_018915.4 | ENSP00000378077.2 | |||
PCDHGA1 | ENST00000517417.3 | c.2421+11388A>C | intron_variant | Intron 1 of 3 | 1 | NM_018912.3 | ENSP00000431083.1 |
Frequencies
GnomAD3 genomes AF: 0.141 AC: 21480AN: 152072Hom.: 2094 Cov.: 33
GnomAD3 exomes AF: 0.0960 AC: 23883AN: 248740Hom.: 1549 AF XY: 0.0952 AC XY: 12860AN XY: 135144
GnomAD4 exome AF: 0.0910 AC: 133041AN: 1461632Hom.: 6975 Cov.: 34 AF XY: 0.0902 AC XY: 65569AN XY: 727094
GnomAD4 genome AF: 0.141 AC: 21525AN: 152190Hom.: 2105 Cov.: 33 AF XY: 0.140 AC XY: 10440AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:1
This variant is associated with the following publications: (PMID: 29409727) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at