rs199702403
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001184880.2(PCDH19):c.3120T>C(p.Asp1040=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,209,586 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000012 ( 0 hom. 5 hem. )
Consequence
PCDH19
NM_001184880.2 synonymous
NM_001184880.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.94
Genes affected
PCDH19 (HGNC:14270): (protocadherin 19) The protein encoded by this gene is a member of the delta-2 protocadherin subclass of the cadherin superfamily. The encoded protein is thought to be a calcium-dependent cell-adhesion protein that is primarily expressed in the brain. Mutations in this gene on human chromosome X are associated with sporadic infantile epileptic encephalopathy and to a female-restricted form of epilepsy (EFMR; also known as PCDH19RE). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant X-100296604-A-G is Benign according to our data. Variant chrX-100296604-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 415289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.94 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH19 | NM_001184880.2 | c.3120T>C | p.Asp1040= | synonymous_variant | 6/6 | ENST00000373034.8 | |
PCDH19 | NM_001105243.2 | c.2979T>C | p.Asp993= | synonymous_variant | 5/5 | ||
PCDH19 | NM_020766.3 | c.2976T>C | p.Asp992= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH19 | ENST00000373034.8 | c.3120T>C | p.Asp1040= | synonymous_variant | 6/6 | 1 | NM_001184880.2 | A1 | |
PCDH19 | ENST00000255531.8 | c.2979T>C | p.Asp993= | synonymous_variant | 5/5 | 1 | P5 | ||
PCDH19 | ENST00000420881.6 | c.2976T>C | p.Asp992= | synonymous_variant | 5/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111453Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33621
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GnomAD3 exomes AF: 0.0000496 AC: 9AN: 181381Hom.: 0 AF XY: 0.0000594 AC XY: 4AN XY: 67355
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GnomAD4 exome AF: 0.0000118 AC: 13AN: 1098133Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 363487
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GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111453Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33621
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 01, 2020 | - - |
Developmental and epileptic encephalopathy, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at