rs4853633

chr2-190081598-G-Achr2-190081598-G-C

Variant summary

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

The XM_047446008.1(C2orf88):c.-448+1575G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,074 control chromosomes in the GnomAD database, including 44,629 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 0.76 (44629 hom., cov: 31)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-448+1575G>A		intron_variant
C2orf88	XM_047446009.1	c.-448+1575G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000495546.1	n.271+1575G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115917 AN: 151956 Hom.: 44608 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.763 AC: 115973 AN: 152074 Hom.: 44629 Cov.: 31 AF XY: 0.765 AC XY: 56837 AN XY: 74340

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.734

Alfa AF: 0.792 Hom.: 67675

Bravo AF: 0.751

Asia WGS AF: 0.767 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.33
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4853633; hg19: chr2-190946324;