2-210025195-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152519.4(KANSL1L):āc.2473G>Cā(p.Val825Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,595,724 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 33)
Exomes š: 0.000026 ( 0 hom. )
Consequence
KANSL1L
NM_152519.4 missense
NM_152519.4 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 1.80
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KANSL1L | NM_152519.4 | c.2473G>C | p.Val825Leu | missense_variant | 13/15 | ENST00000281772.14 | NP_689732.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KANSL1L | ENST00000281772.14 | c.2473G>C | p.Val825Leu | missense_variant | 13/15 | 5 | NM_152519.4 | ENSP00000281772.8 | ||
KANSL1L | ENST00000418791.5 | c.2347G>C | p.Val783Leu | missense_variant | 12/14 | 1 | ENSP00000405724.1 | |||
KANSL1L | ENST00000634716.1 | n.*18G>C | non_coding_transcript_exon_variant | 5/7 | 5 | ENSP00000489299.1 | ||||
KANSL1L | ENST00000634716.1 | n.*18G>C | 3_prime_UTR_variant | 5/7 | 5 | ENSP00000489299.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251414Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135878
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GnomAD4 exome AF: 0.0000263 AC: 38AN: 1443540Hom.: 0 Cov.: 27 AF XY: 0.0000292 AC XY: 21AN XY: 719344
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
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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 | Sep 11, 2024 | The c.2473G>C (p.V825L) alteration is located in exon 13 (coding exon 12) of the KANSL1L gene. This alteration results from a G to C substitution at nucleotide position 2473, causing the valine (V) at amino acid position 825 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
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Gain of disorder (P = 0.1062);.;
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