chr20-38517867-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_020336.4(RALGAPB):āc.1284A>Gā(p.Glu428=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000812 in 1,613,914 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0042 ( 3 hom., cov: 32)
Exomes š: 0.00046 ( 11 hom. )
Consequence
RALGAPB
NM_020336.4 synonymous
NM_020336.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.70
Genes affected
RALGAPB (HGNC:29221): (Ral GTPase activating protein non-catalytic subunit beta) Enables protein heterodimerization activity. Predicted to be involved in activation of GTPase activity. Predicted to act upstream of or within Ral protein signal transduction; regulation of exocyst localization; and regulation of protein localization. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 20-38517867-A-G is Benign according to our data. Variant chr20-38517867-A-G is described in ClinVar as [Benign]. Clinvar id is 3033905.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 635 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RALGAPB | NM_020336.4 | c.1284A>G | p.Glu428= | synonymous_variant | 9/30 | ENST00000262879.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RALGAPB | ENST00000262879.11 | c.1284A>G | p.Glu428= | synonymous_variant | 9/30 | 1 | NM_020336.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00417 AC: 634AN: 152136Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00111 AC: 278AN: 251452Hom.: 5 AF XY: 0.000854 AC XY: 116AN XY: 135896
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GnomAD4 exome AF: 0.000462 AC: 676AN: 1461660Hom.: 11 Cov.: 33 AF XY: 0.000389 AC XY: 283AN XY: 727136
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GnomAD4 genome AF: 0.00417 AC: 635AN: 152254Hom.: 3 Cov.: 32 AF XY: 0.00426 AC XY: 317AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RALGAPB-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at