chr7-102104358-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_181552.4(CUX1):c.429A>G(p.Lys143=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000632 in 1,609,916 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00093 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00060 ( 1 hom. )
Consequence
CUX1
NM_181552.4 synonymous
NM_181552.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.15
Genes affected
CUX1 (HGNC:2557): (cut like homeobox 1) The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession. Several alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 7-102104358-A-G is Benign according to our data. Variant chr7-102104358-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2657859.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.15 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000934 (142/152090) while in subpopulation NFE AF= 0.001 (68/68010). AF 95% confidence interval is 0.000808. There are 1 homozygotes in gnomad4. There are 68 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 142 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUX1 | NM_181552.4 | c.429A>G | p.Lys143= | synonymous_variant | 6/24 | ENST00000292535.12 | |
CUX1 | NM_001913.5 | c.462A>G | p.Lys154= | synonymous_variant | 6/23 | ENST00000622516.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUX1 | ENST00000292535.12 | c.429A>G | p.Lys143= | synonymous_variant | 6/24 | 1 | NM_181552.4 | A2 | |
CUX1 | ENST00000622516.6 | c.462A>G | p.Lys154= | synonymous_variant | 6/23 | 1 | NM_001913.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000934 AC: 142AN: 152090Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000372 AC: 92AN: 247582Hom.: 0 AF XY: 0.000395 AC XY: 53AN XY: 134120
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GnomAD4 exome AF: 0.000600 AC: 875AN: 1457826Hom.: 1 Cov.: 33 AF XY: 0.000583 AC XY: 423AN XY: 725422
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GnomAD4 genome ? AF: 0.000934 AC: 142AN: 152090Hom.: 1 Cov.: 31 AF XY: 0.000915 AC XY: 68AN XY: 74278
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | CUX1: BP4 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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