rs8074980

chr17-57933599-G-Achr17-57933599-G-C

Variant summary

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

The NM_001271875.2(CUEDC1):c.-316+21626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,192 control chromosomes in the GnomAD database, including 1,958 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 0.15 (1958 hom., cov: 31)
• Consequence: CUEDC1 NM_001271875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUEDC1	NM_001271875.2	c.-316+21626C>T		intron_variant		ENST00000577830.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUEDC1	ENST00000577830.6	c.-316+21626C>T		intron_variant		1	NM_001271875.2	P1
CUEDC1	ENST00000577840.5	c.-76+21626C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23471 AN: 152074 Hom.: 1958 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.154 AC: 23487 AN: 152192 Hom.: 1958 Cov.: 31 AF XY: 0.149 AC XY: 11121 AN XY: 74428

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0956

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.129

Alfa AF: 0.153 Hom.: 4111

Bravo AF: 0.151

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.7
Dann	Benign	0.43

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: rs8074980; hg19: chr17-56010960;