rs288817

Positions:

• chr2-189962255-G-A

Variant summary

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

The XM_047446008.1(C2orf88):​c.-518+64692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,196 control chromosomes in the GnomAD database, including 1,483 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 0.083 (1483 hom., cov: 32)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-518+64692G>A		intron_variant
C2orf88	XM_047446009.1	c.-518+82577G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000478197.1	n.219+82428G>A		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.201+82428G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12614 AN: 152078 Hom.: 1473 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00148

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152196 Hom.: 1483 Cov.: 32 AF XY: 0.0819 AC XY: 6092 AN XY: 74406

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00150

Gnomad4 OTH AF: 0.0673

Alfa AF: 0.0137 Hom.: 240

Bravo AF: 0.0991

Asia WGS AF: 0.0650 AC: 227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288817; hg19: chr2-190826981;