2-189962297-A-G

Position:

• chr2-189962297-A-G

Variant summary

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

The XM_047446008.1(C2orf88):​c.-518+64734A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,072 control chromosomes in the GnomAD database, including 25,091 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 0.52 (25091 hom., cov: 31)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

C2orf88 (HGNC:28191): (chromosome 2 open reading frame 88) Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be located in plasma membrane. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-518+64734A>G		intron_variant
C2orf88	XM_047446009.1	c.-518+82619A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000478197.1	n.219+82470A>G		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.201+82470A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78978 AN: 151956 Hom.: 25100 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.519 AC: 78966 AN: 152072 Hom.: 25091 Cov.: 31 AF XY: 0.522 AC XY: 38819 AN XY: 74338

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.547

Alfa AF: 0.668 Hom.: 71424

Bravo AF: 0.489

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053163; hg19: chr2-190827023;