rs2318131

Variant names:

• chr2-237025323-A-C
• rs2318131
• ENST00000655155.1:n.1663-45256T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-237025323-A-C
• chr2-237025323-A-G
• chr2-237025323-A-T

Variant summary

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

The NR_186114.3(COPS8-DT):​n.1666+58833T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,096 control chromosomes in the GnomAD database, including 9,110 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 0.34 (9110 hom., cov: 32)
• Consequence: COPS8-DT NR_186114.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 7 publications found

Genes affected

COPS8-DT (HGNC:55816): (COPS8 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186114.3. 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
	COPS8-DT	NR_186114.3		n.1666+58833T>G		intron	N/A
	COPS8-DT	NR_187934.1		n.1666+58833T>G		intron	N/A
	COPS8-DT	NR_187935.1		n.1667-45256T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COPS8-DT	ENST00000655155.1		n.1663-45256T>G		intron	N/A
	COPS8-DT	ENST00000657607.1		n.1614-11377T>G		intron	N/A
	COPS8-DT	ENST00000660650.1		n.1683+58833T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52199 AN: 151978 Hom.: 9110 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.343 AC: 52230 AN: 152096 Hom.: 9110 Cov.: 32 AF XY: 0.343 AC XY: 25476 AN XY: 74354

African (AFR) AF: 0.339 AC: 14067 AN: 41482

American (AMR) AF: 0.353 AC: 5399 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3464

East Asian (EAS) AF: 0.407 AC: 2099 AN: 5162

South Asian (SAS) AF: 0.356 AC: 1712 AN: 4814

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10592

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23660 AN: 67986

Other (OTH) AF: 0.339 AC: 716 AN: 2112

Alfa AF: 0.342 Hom.: 26114

Bravo AF: 0.345

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.14
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2318131; hg19: chr2-237933966;