rs2129905

Positions:

• chr7-130620608-A-G
• chr7-130620608-A-T

Variant summary

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

The NM_012133.6(COPG2):​c.324-3543T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,034 control chromosomes in the GnomAD database, including 16,577 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 0.42 (16577 hom., cov: 32)
• Consequence: COPG2 NM_012133.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

COPG2 (HGNC:2237): (COPI coat complex subunit gamma 2) Predicted to enable structural molecule activity. Involved in intra-Golgi vesicle-mediated transport. Part of COPI vesicle coat. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COPG2	NM_012133.6	c.324-3543T>C		intron_variant		ENST00000425248.5
COPG2	NM_001290033.2	c.324-3543T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COPG2	ENST00000425248.5	c.324-3543T>C		intron_variant		1	NM_012133.6	P1
COPG2	ENST00000330992.8	c.324-3543T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64447 AN: 151916 Hom.: 16576 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.424 AC: 64453 AN: 152034 Hom.: 16577 Cov.: 32 AF XY: 0.429 AC XY: 31843 AN XY: 74298

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.443

Alfa AF: 0.462 Hom.: 2244

Bravo AF: 0.409

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs2129905; hg19: chr7-130305479;