chr4-30722107-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001173523.2(PCDH7):āc.685T>Gā(p.Ser229Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,415,782 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
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.685T>G | p.Ser229Ala | missense_variant | 1/3 | ENST00000695919.1 | |
PCDH7 | NM_032457.4 | c.685T>G | p.Ser229Ala | missense_variant | 1/3 | ||
PCDH7 | NM_002589.4 | c.685T>G | p.Ser229Ala | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH7 | ENST00000695919.1 | c.685T>G | p.Ser229Ala | missense_variant | 1/3 | NM_001173523.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000397 AC: 6AN: 151252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000344 AC: 1AN: 29086Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 15340
GnomAD4 exome AF: 0.00000870 AC: 11AN: 1264420Hom.: 0 Cov.: 31 AF XY: 0.00000813 AC XY: 5AN XY: 614634
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151362Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 73944
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.685T>G (p.S229A) alteration is located in exon 1 (coding exon 1) of the PCDH7 gene. This alteration results from a T to G substitution at nucleotide position 685, causing the serine (S) at amino acid position 229 to be replaced by an alanine (A). 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