rs2318131

Positions:

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

Variant summary

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

The ENST00000662924.1(COPS8-DT):​n.1613+58833T>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 0.343 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 ENST00000662924.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

Genes affected

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

LOC105373951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373951	XR_007088142.1	n.1666+58833T>G		intron_variant, non_coding_transcript_variant
LOC105373951	XR_007088141.1	n.1667-11377T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COPS8-DT	ENST00000662924.1	n.1613+58833T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.339

Alfa AF: 0.338 Hom.: 11480

Bravo AF: 0.345

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2318131; hg19: chr2-237933966;