7-102243424-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181552.4(CUX1):c.3887+3840A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,820 control chromosomes in the GnomAD database, including 12,497 homozygotes. 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 0.38 (12497 hom., cov: 30)
• Consequence: CUX1 NM_181552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

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]

LOC124901711 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUX1	NM_001913.5	c.1256-29942A>G		intron_variant		ENST00000622516.6
CUX1	NM_181552.4	c.3887+3840A>G		intron_variant		ENST00000292535.12
LOC124901711	XR_007060458.1	n.83-520T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUX1	ENST00000292535.12	c.3887+3840A>G		intron_variant		1	NM_181552.4	A2
CUX1	ENST00000622516.6	c.1256-29942A>G		intron_variant		1	NM_001913.5

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57858 AN: 151702 Hom.: 12498 Cov.: 30

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.381 AC: 57867 AN: 151820 Hom.: 12497 Cov.: 30 AF XY: 0.389 AC XY: 28887 AN XY: 74204

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.392

Alfa AF: 0.403 Hom.: 9252

Bravo AF: 0.372

Asia WGS AF: 0.621 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.70

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

Other links and lift over

dbSNP: rs427534; hg19: chr7-101886704;