Variant 7-102070310-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_181552.4(CUX1):c.190-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 1,582,904 control chromosomes in the GnomAD database, including 550,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.84 ( 53548 hom., cov: 33)

Exomes 𝑓: 0.83 ( 497329 hom. )

Consequence

CUX1
NM_181552.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.231

Variant links:

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]

CUX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 7-102070310-T-C is Benign according to our data. Variant chr7-102070310-T-C is described in ClinVar as [Benign]. Clinvar id is 1255424.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUX1	NM_001913.5 linkuse as main transcript	c.223-29T>C		intron_variant		ENST00000622516.6
CUX1	NM_181552.4 linkuse as main transcript	c.190-29T>C		intron_variant		ENST00000292535.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUX1	ENST00000292535.12 linkuse as main transcript	c.190-29T>C		intron_variant		1	NM_181552.4	A2	P39880-1
CUX1	ENST00000622516.6 linkuse as main transcript	c.223-29T>C		intron_variant		1	NM_001913.5		Q13948-1

Frequencies

GnomAD3 genomes

AF:

0.838

AC:

127409

AN:

152064

Hom.:

53517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.842

Gnomad AMI

AF:

0.705

Gnomad AMR

AF:

0.848

Gnomad ASJ

AF:

0.770

Gnomad EAS

AF:

0.991

Gnomad SAS

AF:

0.875

Gnomad FIN

AF:

0.879

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.818

Gnomad OTH

AF:

0.821

GnomAD3 exomes

AF:

0.854

AC:

205620

AN:

240842

Hom.:

88189

AF XY:

0.851

AC XY:

111663

AN XY:

131234

show subpopulations

Gnomad AFR exome

AF:

0.842

Gnomad AMR exome

AF:

0.901

Gnomad ASJ exome

AF:

0.778

Gnomad EAS exome

AF:

0.991

Gnomad SAS exome

AF:

0.869

Gnomad FIN exome

AF:

0.883

Gnomad NFE exome

AF:

0.819

Gnomad OTH exome

AF:

0.822

GnomAD4 exome

AF:

0.833

AC:

1191130

AN:

1430722

Hom.:

497329

Cov.:

AF XY:

0.833

AC XY:

594143

AN XY:

713526

show subpopulations

Gnomad4 AFR exome

AF:

0.846

Gnomad4 AMR exome

AF:

0.895

Gnomad4 ASJ exome

AF:

0.775

Gnomad4 EAS exome

AF:

0.992

Gnomad4 SAS exome

AF:

0.870

Gnomad4 FIN exome

AF:

0.881

Gnomad4 NFE exome

AF:

0.820

Gnomad4 OTH exome

AF:

0.833

GnomAD4 genome

AF:

0.838

AC:

127492

AN:

152182

Hom.:

53548

Cov.:

AF XY:

0.842

AC XY:

62647

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.842

Gnomad4 AMR

AF:

0.849

Gnomad4 ASJ

AF:

0.770

Gnomad4 EAS

AF:

0.991

Gnomad4 SAS

AF:

0.874

Gnomad4 FIN

AF:

0.879

Gnomad4 NFE

AF:

0.818

Gnomad4 OTH

AF:

0.824

Alfa

AF:

0.796

Hom.:

5668

Bravo

AF:

0.838

Asia WGS

AF:

0.916

AC:

3186

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Global developmental delay with or without impaired intellectual development

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.87

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over