chr9-5920046-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001017969.3(KIAA2026):āc.5950C>Gā(p.Gln1984Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000632 in 1,613,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000092 ( 0 hom., cov: 32)
Exomes š: 0.000060 ( 0 hom. )
Consequence
KIAA2026
NM_001017969.3 missense
NM_001017969.3 missense
Scores
1
2
16
Clinical Significance
Conservation
PhyloP100: 6.66
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.099923134).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA2026 | NM_001017969.3 | c.5950C>G | p.Gln1984Glu | missense_variant | 8/8 | ENST00000399933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2026 | ENST00000399933.8 | c.5950C>G | p.Gln1984Glu | missense_variant | 8/8 | 5 | NM_001017969.3 | P4 | |
KIAA2026 | ENST00000381461.6 | c.5860C>G | p.Gln1954Glu | missense_variant | 7/7 | 5 | A2 | ||
KIAA2026 | ENST00000436015.6 | c.554+498C>G | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000540714.1 | c.*3537C>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152180Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000963 AC: 24AN: 249102Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135134
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GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461678Hom.: 0 Cov.: 35 AF XY: 0.0000660 AC XY: 48AN XY: 727132
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74338
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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 | Nov 21, 2022 | The c.5950C>G (p.Q1984E) alteration is located in exon 8 (coding exon 8) of the KIAA2026 gene. This alteration results from a C to G substitution at nucleotide position 5950, causing the glutamine (Q) at amino acid position 1984 to be replaced by a glutamic acid (E). 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
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
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