chr5-140807817-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018907.4(PCDHA4):c.630A>C(p.Leu210Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018907.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHA4 | NM_018907.4 | c.630A>C | p.Leu210Phe | missense_variant | 1/4 | ENST00000530339.2 | |
PCDHA1 | NM_018900.4 | c.2394+19133A>C | intron_variant | ENST00000504120.4 | |||
PCDHA2 | NM_018905.3 | c.2388+10465A>C | intron_variant | ENST00000526136.2 | |||
PCDHA3 | NM_018906.3 | c.2394+4226A>C | intron_variant | ENST00000522353.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHA4 | ENST00000530339.2 | c.630A>C | p.Leu210Phe | missense_variant | 1/4 | 1 | NM_018907.4 | P1 | |
PCDHA1 | ENST00000504120.4 | c.2394+19133A>C | intron_variant | 1 | NM_018900.4 | P1 | |||
PCDHA3 | ENST00000522353.3 | c.2394+4226A>C | intron_variant | 1 | NM_018906.3 | P1 | |||
PCDHA2 | ENST00000526136.2 | c.2388+10465A>C | intron_variant | 1 | NM_018905.3 | P1 | |||
ENST00000655235.1 | n.658-18963T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251156Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135882
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461864Hom.: 0 Cov.: 36 AF XY: 0.000128 AC XY: 93AN XY: 727230
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.630A>C (p.L210F) alteration is located in exon 1 (coding exon 1) of the PCDHA4 gene. This alteration results from a A to C substitution at nucleotide position 630, causing the leucine (L) at amino acid position 210 to be replaced by a phenylalanine (F). 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