rs1503122

Variant names:

• chr1-176280573-T-G
• rs1503122
• ENST00000654248.1:n.621+15455T>G

Variant summary

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

The ENST00000654248.1(COP1-DT):​n.621+15455T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,254 control chromosomes in the GnomAD database, including 1,885 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 (1885 hom., cov: 33)
• Consequence: COP1-DT ENST00000654248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 6 publications found

Genes affected

COP1-DT (HGNC:55666): (COP1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COP1-DT	ENST00000654248.1	n.621+15455T>G		intron_variant	Intron 4 of 5
COP1-DT	ENST00000660913.1	n.633+15455T>G		intron_variant	Intron 5 of 5
COP1-DT	ENST00000701212.1	n.702+15455T>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22892 AN: 152136 Hom.: 1884 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.150 AC: 22901 AN: 152254 Hom.: 1885 Cov.: 33 AF XY: 0.147 AC XY: 10968 AN XY: 74460

African (AFR) AF: 0.134 AC: 5575 AN: 41548

American (AMR) AF: 0.212 AC: 3237 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5186

South Asian (SAS) AF: 0.120 AC: 580 AN: 4832

European-Finnish (FIN) AF: 0.141 AC: 1499 AN: 10602

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11002 AN: 68000

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.174 Hom.: 3591

Bravo AF: 0.158

Asia WGS AF: 0.0720 AC: 252 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1503122; hg19: chr1-176249709;