rs1725604

Positions:

• chr7-102270864-C-T

Variant summary

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

The NM_001913.5(CUX1):​c.1256-2502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,070 control chromosomes in the GnomAD database, including 29,924 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 0.62 (29924 hom., cov: 32)
• Consequence: CUX1 NM_001913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUX1	NM_001913.5	c.1256-2502C>T		intron_variant		ENST00000622516.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUX1	ENST00000622516.6	c.1256-2502C>T		intron_variant		1	NM_001913.5

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94821 AN: 151952 Hom.: 29887 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.624 AC: 94914 AN: 152070 Hom.: 29924 Cov.: 32 AF XY: 0.617 AC XY: 45882 AN XY: 74328

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.605

Alfa AF: 0.608 Hom.: 16298

Bravo AF: 0.637

Asia WGS AF: 0.610 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1725604; hg19: chr7-101914135;