Variant chr7-102097330-C-A 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.269-34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 1,582,300 control chromosomes in the GnomAD database, including 261,486 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 29713 hom., cov: 32)

Exomes 𝑓: 0.56 ( 231773 hom. )

Consequence

CUX1
NM_181552.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.775

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=-0.84).

BP6

Variant 7-102097330-C-A is Benign according to our data. Variant chr7-102097330-C-A is described in ClinVar as [Benign]. Clinvar id is 1255426.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 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.302-34C>A		intron_variant		ENST00000622516.6
CUX1	NM_181552.4 linkuse as main transcript	c.269-34C>A		intron_variant		ENST00000292535.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUX1	ENST00000292535.12 linkuse as main transcript	c.269-34C>A		intron_variant		1	NM_181552.4	A2	P39880-1
CUX1	ENST00000622516.6 linkuse as main transcript	c.302-34C>A		intron_variant		1	NM_001913.5		Q13948-1

Frequencies

GnomAD3 genomes

AF:

0.606

AC:

91758

AN:

151460

Hom.:

29671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.621

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.0486

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.514

Gnomad MID

AF:

0.674

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.594

GnomAD3 exomes

AF:

0.517

AC:

117402

AN:

226910

Hom.:

33527

AF XY:

0.519

AC XY:

63760

AN XY:

122812

show subpopulations

Gnomad AFR exome

AF:

0.799

Gnomad AMR exome

AF:

0.405

Gnomad ASJ exome

AF:

0.642

Gnomad EAS exome

AF:

0.0495

Gnomad SAS exome

AF:

0.476

Gnomad FIN exome

AF:

0.503

Gnomad NFE exome

AF:

0.582

Gnomad OTH exome

AF:

0.555

GnomAD4 exome

AF:

0.558

AC:

798941

AN:

1430724

Hom.:

231773

Cov.:

AF XY:

0.556

AC XY:

395057

AN XY:

710532

show subpopulations

Gnomad4 AFR exome

AF:

0.807

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.643

Gnomad4 EAS exome

AF:

0.0481

Gnomad4 SAS exome

AF:

0.479

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.581

Gnomad4 OTH exome

AF:

0.557

GnomAD4 genome

AF:

0.606

AC:

91860

AN:

151576

Hom.:

29713

Cov.:

AF XY:

0.595

AC XY:

44088

AN XY:

74088

show subpopulations

Gnomad4 AFR

AF:

0.793

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.0491

Gnomad4 SAS

AF:

0.449

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.596

Alfa

AF:

0.600

Hom.:

5282

Bravo

AF:

0.613

Asia WGS

AF:

0.308

AC:

1075

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

-0.84

CADD

Benign

0.81

DANN

Benign

0.74

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