chr1-176167350-G-T

Variant names:

• chr1-176167350-G-T
• rs11587785
• NM_022457.7:c.566-3459C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_022457.7(COP1):​c.566-3459C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 152,280 control chromosomes in the GnomAD database, including 117 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 0.033 (117 hom., cov: 32)
• Consequence: COP1 NM_022457.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 1 publications found

Genes affected

COP1 (HGNC:17440): (COP1 E3 ubiquitin ligase) Enables ubiquitin protein ligase activity. Involved in positive regulation of proteasomal ubiquitin-dependent protein catabolic process; proteasome-mediated ubiquitin-dependent protein catabolic process; and response to ionizing radiation. Part of Cul4A-RING E3 ubiquitin ligase complex. [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).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0327 (4972/152280) while in subpopulation NFE AF = 0.0473 (3216/68036). AF 95% confidence interval is 0.0459. There are 117 homozygotes in GnomAd4. There are 2435 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 4972 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022457.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COP1	NM_022457.7	MANE Select	c.566-3459C>A		intron	N/A	NP_071902.2
	COP1	NM_001001740.4		c.566-3459C>A		intron	N/A	NP_001001740.1	Q8NHY2-2
	COP1	NM_001286644.2		c.42+8560C>A		intron	N/A	NP_001273573.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COP1	ENST00000367669.8	TSL:1 MANE Select	c.566-3459C>A		intron	N/A	ENSP00000356641.3	Q8NHY2-1
	COP1	ENST00000308769.12	TSL:1	c.566-3459C>A		intron	N/A	ENSP00000310943.8	Q8NHY2-2
	COP1	ENST00000367667.5	TSL:1	n.277+8560C>A		intron	N/A	ENSP00000356639.1	H0Y340

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4978 AN: 152162 Hom.: 117 Cov.: 32

Gnomad AFR AF: 0.00753

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0472

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0327 AC: 4972 AN: 152280 Hom.: 117 Cov.: 32 AF XY: 0.0327 AC XY: 2435 AN XY: 74456

African (AFR) AF: 0.00751 AC: 312 AN: 41538

American (AMR) AF: 0.0263 AC: 403 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5184

South Asian (SAS) AF: 0.0431 AC: 208 AN: 4822

European-Finnish (FIN) AF: 0.0415 AC: 440 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0473 AC: 3216 AN: 68036

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0385 Hom.: 20

Bravo AF: 0.0299

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism

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: rs11587785; hg19: chr1-176136486;