rs61752337
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000379562.9(KIN):c.1136G>A(p.Arg379His) variant causes a missense change. The variant allele was found at a frequency of 0.000121 in 1,585,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
KIN
ENST00000379562.9 missense
ENST00000379562.9 missense
Scores
1
11
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.40
Genes affected
KIN (HGNC:6327): (Kin17 DNA and RNA binding protein) The protein encoded by this gene is a nuclear protein that forms intranuclear foci during proliferation and is redistributed in the nucleoplasm during the cell cycle. Short-wave ultraviolet light provokes the relocalization of the protein, suggesting its participation in the cellular response to DNA damage. Originally selected based on protein-binding with RecA antibodies, the mouse protein presents a limited similarity with a functional domain of the bacterial RecA protein, a characteristic shared by this human ortholog. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
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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 |
---|---|---|---|---|---|---|---|---|
KIN | NM_012311.4 | c.1136G>A | p.Arg379His | missense_variant | 13/13 | ENST00000379562.9 | NP_036443.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIN | ENST00000379562.9 | c.1136G>A | p.Arg379His | missense_variant | 13/13 | 1 | NM_012311.4 | ENSP00000368881 | P1 | |
KIN | ENST00000463666.5 | n.387G>A | non_coding_transcript_exon_variant | 6/6 | 3 | |||||
KIN | ENST00000471320.5 | n.594G>A | non_coding_transcript_exon_variant | 5/5 | 2 | |||||
KIN | ENST00000498098.1 | c.322-2057G>A | intron_variant, NMD_transcript_variant | 3 | ENSP00000473950 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152074Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000850 AC: 20AN: 235196Hom.: 0 AF XY: 0.0000864 AC XY: 11AN XY: 127244
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GnomAD4 exome AF: 0.000125 AC: 179AN: 1433226Hom.: 0 Cov.: 26 AF XY: 0.000131 AC XY: 93AN XY: 712348
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GnomAD4 genome AF: 0.0000855 AC: 13AN: 152074Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74264
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 16
Find out detailed SpliceAI scores and Pangolin per-transcript scores at