X-55031184-G-C
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The XM_011530785.3(PAGE2B):c.61+1512G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00655 in 181,091 control chromosomes in the GnomAD database, including 3 homozygotes. There are 263 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 0.0065 ( 3 hom., 175 hem., cov: 22)
Exomes 𝑓: 0.0067 ( 0 hom. 88 hem. )
Consequence
PAGE2B
XM_011530785.3 intron
XM_011530785.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.404
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant X-55031184-G-C is Benign according to our data. Variant chrX-55031184-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 10480.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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PAGE2B | XM_011530785.3 | c.61+1512G>C | intron_variant | ||||
PAGE2B | XM_011530786.4 | c.7+209G>C | intron_variant |
Ensembl
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Frequencies
GnomAD3 genomes AF: 0.00647 AC: 720AN: 111336Hom.: 3 Cov.: 22 AF XY: 0.00522 AC XY: 175AN XY: 33542
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GnomAD4 exome AF: 0.00669 AC: 466AN: 69705Hom.: 0 AF XY: 0.00598 AC XY: 88AN XY: 14711
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GnomAD4 genome AF: 0.00646 AC: 720AN: 111386Hom.: 3 Cov.: 22 AF XY: 0.00521 AC XY: 175AN XY: 33602
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 26, 2021 | Nucleotide substitution has no predicted effect on splicing and is not conserved across species; This variant is associated with the following publications: (PMID: 23935018, 25910213, 12663458, 32641076) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ALAS2: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
X-linked sideroblastic anemia 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 2003 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at