rs8074980

Variant names:

• chr17-57933599-G-A
• rs8074980
• NM_001271875.2:c.-316+21626C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-57933599-G-A
• chr17-57933599-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 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=-0.9).
• 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 rank	MANE	Protein	UniProt
CUEDC1	NM_001271875.2	c.-316+21626C>T		intron_variant	Intron 1 of 10	ENST00000577830.6	NP_001258804.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUEDC1	ENST00000577830.6	c.-316+21626C>T		intron_variant	Intron 1 of 10	1	NM_001271875.2	ENSP00000462717.1
CUEDC1	ENST00000577840.5	c.-76+21626C>T		intron_variant	Intron 1 of 9	5		ENSP00000463666.1

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

African (AFR) AF: 0.183 AC: 7582 AN: 41520

American (AMR) AF: 0.0956 AC: 1461 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.149 AC: 720 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10602

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11311 AN: 67994

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.156 Hom.: 6315

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
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8074980; hg19: chr17-56010960;