rs1503122

chr1-176280573-T-G

Variant summary

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

The ENST00000654248.1(COP1-DT):n.621+15455T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COP1-DT	ENST00000654248.1	n.621+15455T>G		intron_variant, non_coding_transcript_variant
COP1-DT	ENST00000660913.1	n.633+15455T>G		intron_variant, non_coding_transcript_variant
COP1-DT	ENST00000701212.1	n.702+15455T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.161

Alfa AF: 0.174 Hom.: 2700

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1503122; hg19: chr1-176249709;