X-133302957-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001448.3(GPC4):c.1581C>T(p.Ala527=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,209,561 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 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 0.0000090 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )
Consequence
GPC4
NM_001448.3 synonymous
NM_001448.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.154
Genes affected
GPC4 (HGNC:4452): (glypican 4) Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. The GPC4 gene is adjacent to the 3' end of GPC3 and may also play a role in Simpson-Golabi-Behmel syndrome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant X-133302957-G-A is Benign according to our data. Variant chrX-133302957-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 743176.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.154 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC4 | NM_001448.3 | c.1581C>T | p.Ala527= | synonymous_variant | 9/9 | ENST00000370828.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC4 | ENST00000370828.4 | c.1581C>T | p.Ala527= | synonymous_variant | 9/9 | 1 | NM_001448.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111565Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33755
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GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183045Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67627
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GnomAD4 exome AF: 0.00000455 AC: 5AN: 1097996Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 2AN XY: 363352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at