5-141331554-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000517417.3(PCDHGA1):āc.870A>Cā(p.Gln290His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000517417.3 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 |
---|---|---|---|---|---|---|---|---|
PCDHGA1 | NM_018912.3 | c.870A>C | p.Gln290His | missense_variant | 1/4 | ENST00000517417.3 | NP_061735.1 | |
PCDHGA1 | NM_031993.2 | c.870A>C | p.Gln290His | missense_variant | 1/1 | NP_114382.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHGA1 | ENST00000517417.3 | c.870A>C | p.Gln290His | missense_variant | 1/4 | 1 | NM_018912.3 | ENSP00000431083 | P1 | |
PCDHGA1 | ENST00000378105.4 | c.870A>C | p.Gln290His | missense_variant | 1/1 | ENSP00000367345 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251170Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135762
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461840Hom.: 0 Cov.: 37 AF XY: 0.0000124 AC XY: 9AN XY: 727220
GnomAD4 genome AF: 0.000204 AC: 31AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.870A>C (p.Q290H) alteration is located in exon 1 (coding exon 1) of the PCDHGA1 gene. This alteration results from a A to C substitution at nucleotide position 870, causing the glutamine (Q) at amino acid position 290 to be replaced by a histidine (H). 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