2-87782669-A-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001078170.3(RGPD2):c.4355T>A(p.Ile1452Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 5)
Exomes 𝑓: 0.00015 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
RGPD2
NM_001078170.3 missense
NM_001078170.3 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 3.23
Genes affected
RGPD2 (HGNC:32415): (RANBP2 like and GRIP domain containing 2) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.14524037).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGPD2 | NM_001078170.3 | c.4355T>A | p.Ile1452Asn | missense_variant | 20/23 | ENST00000398146.5 | NP_001071638.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGPD2 | ENST00000398146.5 | c.4355T>A | p.Ile1452Asn | missense_variant | 20/23 | 1 | NM_001078170.3 | ENSP00000381214.3 | ||
RGPD2 | ENST00000494592.1 | n.1T>A | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 20258Hom.: 0 Cov.: 5 FAILED QC
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GnomAD3 exomes AF: 0.0000378 AC: 2AN: 52894Hom.: 0 AF XY: 0.0000376 AC XY: 1AN XY: 26578
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000146 AC: 102AN: 700802Hom.: 1 Cov.: 9 AF XY: 0.000146 AC XY: 52AN XY: 357072
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000987 AC: 2AN: 20258Hom.: 0 Cov.: 5 AF XY: 0.000106 AC XY: 1AN XY: 9422
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.4355T>A (p.I1452N) alteration is located in exon 20 (coding exon 20) of the RGPD2 gene. This alteration results from a T to A substitution at nucleotide position 4355, causing the isoleucine (I) at amino acid position 1452 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;.
Vest4
MutPred
Gain of disorder (P = 0.0268);Gain of disorder (P = 0.0268);
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
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