1-89191291-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_052941.5(GBP4):c.886C>T(p.Leu296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0091 in 1,613,772 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0092 ( 86 hom. )
Consequence
GBP4
NM_052941.5 synonymous
NM_052941.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.224
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 1-89191291-G-A is Benign according to our data. Variant chr1-89191291-G-A is described in ClinVar as [Benign]. Clinvar id is 781583.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.224 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00924 (13498/1461472) while in subpopulation MID AF= 0.0248 (143/5768). AF 95% confidence interval is 0.0215. There are 86 homozygotes in gnomad4_exome. There are 6703 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBP4 | NM_052941.5 | c.886C>T | p.Leu296= | synonymous_variant | 6/11 | ENST00000355754.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBP4 | ENST00000355754.7 | c.886C>T | p.Leu296= | synonymous_variant | 6/11 | 1 | NM_052941.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00783 AC: 1192AN: 152182Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00775 AC: 1948AN: 251392Hom.: 16 AF XY: 0.00801 AC XY: 1088AN XY: 135870
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GnomAD4 exome AF: 0.00924 AC: 13498AN: 1461472Hom.: 86 Cov.: 31 AF XY: 0.00922 AC XY: 6703AN XY: 726970
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GnomAD4 genome AF: 0.00782 AC: 1191AN: 152300Hom.: 8 Cov.: 32 AF XY: 0.00712 AC XY: 530AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 20, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at