4-30721518-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001173523.2(PCDH7):āc.96G>Cā(p.Gln32His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,600,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001173523.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PCDH7 | NM_001173523.2 | c.96G>C | p.Gln32His | missense_variant | 1/3 | ENST00000695919.1 | |
PCDH7 | NM_032457.4 | c.96G>C | p.Gln32His | missense_variant | 1/3 | ||
PCDH7 | NM_002589.4 | c.96G>C | p.Gln32His | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH7 | ENST00000695919.1 | c.96G>C | p.Gln32His | missense_variant | 1/3 | NM_001173523.2 | A1 | ||
ENST00000660555.1 | n.453C>G | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes AF: 0.000236 AC: 36AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000493 AC: 115AN: 233246Hom.: 0 AF XY: 0.000460 AC XY: 59AN XY: 128226
GnomAD4 exome AF: 0.000232 AC: 336AN: 1448738Hom.: 0 Cov.: 32 AF XY: 0.000241 AC XY: 174AN XY: 721020
GnomAD4 genome AF: 0.000236 AC: 36AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.96G>C (p.Q32H) alteration is located in exon 1 (coding exon 1) of the PCDH7 gene. This alteration results from a G to C substitution at nucleotide position 96, causing the glutamine (Q) at amino acid position 32 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