2-87772238-G-A
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001078170.3(RGPD2):c.5167C>T(p.Leu1723Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 16)
Exomes 𝑓: 0.000050 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RGPD2
NM_001078170.3 missense
NM_001078170.3 missense
Scores
2
2
15
Clinical Significance
Conservation
PhyloP100: 2.37
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 -1 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.2722708).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGPD2 | NM_001078170.3 | c.5167C>T | p.Leu1723Phe | missense_variant | 22/23 | ENST00000398146.5 | NP_001071638.2 | |
RGPD2 | NM_001393613.1 | c.5008C>T | p.Leu1670Phe | missense_variant | 22/23 | NP_001380542.1 | ||
RGPD2 | XM_017004845.2 | c.5401C>T | p.Leu1801Phe | missense_variant | 25/26 | XP_016860334.2 | ||
RGPD2 | XM_047445734.1 | c.5326C>T | p.Leu1776Phe | missense_variant | 24/25 | XP_047301690.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 5AN: 125948Hom.: 0 Cov.: 16 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000499 AC: 63AN: 1263376Hom.: 0 Cov.: 19 AF XY: 0.0000394 AC XY: 25AN XY: 634244
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000397 AC: 5AN: 125948Hom.: 0 Cov.: 16 AF XY: 0.0000664 AC XY: 4AN XY: 60272
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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 | Oct 29, 2021 | The c.5167C>T (p.L1723F) alteration is located in exon 22 (coding exon 22) of the RGPD2 gene. This alteration results from a C to T substitution at nucleotide position 5167, causing the leucine (L) at amino acid position 1723 to be replaced by a phenylalanine (F). 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
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Pathogenic
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Pathogenic
D;.
Sift4G
Benign
T;.
Vest4
MVP
ClinPred
T
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