chr10-100190937-A-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001278.5(CHUK):ā€‹c.2140T>Cā€‹(p.Leu714=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CHUK
NM_001278.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.65
Variant links:
Genes affected
CHUK (HGNC:1974): (component of inhibitor of nuclear factor kappa B kinase complex) This gene encodes a member of the serine/threonine protein kinase family. The encoded protein, a component of a cytokine-activated protein complex that is an inhibitor of the essential transcription factor NF-kappa-B complex, phosphorylates sites that trigger the degradation of the inhibitor via the ubiquination pathway, thereby activating the transcription factor. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 10-100190937-A-G is Benign according to our data. Variant chr10-100190937-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1667719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.65 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHUKNM_001278.5 linkuse as main transcriptc.2140T>C p.Leu714= synonymous_variant 20/21 ENST00000370397.8 NP_001269.3
CHUKNM_001320928.2 linkuse as main transcriptc.2123T>C p.Phe708Ser missense_variant 20/21 NP_001307857.1
CHUKXM_047424542.1 linkuse as main transcriptc.2123T>C p.Phe708Ser missense_variant 20/21 XP_047280498.1
CHUKXM_047424540.1 linkuse as main transcriptc.2140T>C p.Leu714= synonymous_variant 20/21 XP_047280496.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHUKENST00000370397.8 linkuse as main transcriptc.2140T>C p.Leu714= synonymous_variant 20/211 NM_001278.5 ENSP00000359424 P1
CHUKENST00000590930.5 linkuse as main transcriptn.3516T>C non_coding_transcript_exon_variant 2/31
CHUKENST00000585551.1 linkuse as main transcriptn.158T>C non_coding_transcript_exon_variant 2/23
CHUKENST00000588656.1 linkuse as main transcriptn.171T>C non_coding_transcript_exon_variant 3/43

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1459560
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
726266
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 06, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
7.4
DANN
Benign
0.86
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1845183136; hg19: chr10-101950694; API