chr9-5919718-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001017969.3(KIAA2026):c.6278C>T(p.Ser2093Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000011 in 1,459,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
KIAA2026
NM_001017969.3 missense
NM_001017969.3 missense
Scores
1
7
11
Clinical Significance
Conservation
PhyloP100: 5.26
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3989398).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA2026 | NM_001017969.3 | c.6278C>T | p.Ser2093Leu | missense_variant | 8/8 | ENST00000399933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2026 | ENST00000399933.8 | c.6278C>T | p.Ser2093Leu | missense_variant | 8/8 | 5 | NM_001017969.3 | P4 | |
KIAA2026 | ENST00000381461.6 | c.6188C>T | p.Ser2063Leu | missense_variant | 7/7 | 5 | A2 | ||
KIAA2026 | ENST00000436015.6 | c.554+826C>T | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000540714.1 | c.*3865C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000817 AC: 2AN: 244720Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132762
GnomAD3 exomes
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2
AN:
244720
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AN XY:
132762
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GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459660Hom.: 0 Cov.: 35 AF XY: 0.0000152 AC XY: 11AN XY: 725914
GnomAD4 exome
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16
AN:
1459660
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Cov.:
35
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11
AN XY:
725914
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Asia WGS
AF:
AC:
2
AN:
3478
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 | May 18, 2022 | The c.6278C>T (p.S2093L) alteration is located in exon 8 (coding exon 8) of the KIAA2026 gene. This alteration results from a C to T substitution at nucleotide position 6278, causing the serine (S) at amino acid position 2093 to be replaced by a leucine (L). 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
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
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
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Loss of glycosylation at S2093 (P = 0.0025);.;
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at