rs1017528

Variant names:

• chr17-57935190-T-C
• rs1017528
• NM_001271875.2:c.-316+20035A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-57935190-T-C
• chr17-57935190-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577830.6(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 ENST00000577830.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577830.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUEDC1	NM_001271875.2	MANE Select	c.-316+20035A>G		intron	N/A	NP_001258804.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUEDC1	ENST00000577830.6	TSL:1 MANE Select	c.-316+20035A>G		intron	N/A	ENSP00000462717.1
	CUEDC1	ENST00000577840.5	TSL:5	c.-76+20035A>G		intron	N/A	ENSP00000463666.1

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

African (AFR) AF: 0.311 AC: 12904 AN: 41446

American (AMR) AF: 0.783 AC: 11965 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2724 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5098 AN: 5190

South Asian (SAS) AF: 0.708 AC: 3415 AN: 4824

European-Finnish (FIN) AF: 0.759 AC: 8020 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52152 AN: 68000

Other (OTH) AF: 0.728 AC: 1533 AN: 2106

Alfa AF: 0.732 Hom.: 128196

Bravo AF: 0.641

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1017528; hg19: chr17-56012551;