rs1017528

chr17-57935190-T-Cchr17-57935190-T-G

Variant summary

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

The NM_001271875.2(CUEDC1):c.-316+20035A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,084 control chromosomes in the GnomAD database, including 35,486 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 0.65 (35486 hom., cov: 32)
• Consequence: CUEDC1 NM_001271875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

Genes affected

CUEDC1 (HGNC:31350): (CUE domain containing 1) Predicted to enable ubiquitin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUEDC1	NM_001271875.2	c.-316+20035A>G		intron_variant		ENST00000577830.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUEDC1	ENST00000577830.6	c.-316+20035A>G		intron_variant		1	NM_001271875.2	P1
CUEDC1	ENST00000577840.5	c.-76+20035A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98666 AN: 151966 Hom.: 35473 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.649 AC: 98705 AN: 152084 Hom.: 35486 Cov.: 32 AF XY: 0.654 AC XY: 48626 AN XY: 74346

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.728

Alfa AF: 0.756 Hom.: 55358

Bravo AF: 0.641

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	12
Dann	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1017528; hg19: chr17-56012551;