chr17-42990902-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173079.5(RUNDC1):c.1028G>A(p.Arg343Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000391 in 1,609,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000037 ( 0 hom. )
Consequence
RUNDC1
NM_173079.5 missense
NM_173079.5 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 5.50
Genes affected
RUNDC1 (HGNC:25418): (RUN domain containing 1) This gene encodes a protein that contains a RUN (RPIP8, UNC-14 and NESCA) domain and a coiled coil domain. The encoded protein may negatively regulate p53 transcriptional activity. This gene is a potential candidate gene for predisposition to glioma in humans. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06322572).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNDC1 | NM_173079.5 | c.1028G>A | p.Arg343Gln | missense_variant | 5/5 | ENST00000361677.6 | |
RUNDC1 | NM_001321381.3 | c.1034G>A | p.Arg345Gln | missense_variant | 6/6 | ||
RUNDC1 | NM_001394222.1 | c.1031G>A | p.Arg344Gln | missense_variant | 5/5 | ||
RUNDC1 | XM_005257078.5 | c.1037G>A | p.Arg346Gln | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNDC1 | ENST00000361677.6 | c.1028G>A | p.Arg343Gln | missense_variant | 5/5 | 1 | NM_173079.5 | P1 | |
RUNDC1 | ENST00000589705.1 | c.*34G>A | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152240Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.0000760 AC: 19AN: 250082Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135380
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GnomAD4 exome AF: 0.0000371 AC: 54AN: 1457374Hom.: 0 Cov.: 32 AF XY: 0.0000483 AC XY: 35AN XY: 724060
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152358Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74500
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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 | Jul 05, 2022 | The c.1028G>A (p.R343Q) alteration is located in exon 5 (coding exon 5) of the RUNDC1 gene. This alteration results from a G to A substitution at nucleotide position 1028, causing the arginine (R) at amino acid position 343 to be replaced by a glutamine (Q). 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
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
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