2-189987439-C-T

Position:

• chr2-189987439-C-T

Variant summary

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

The XM_047446008.1(C2orf88):​c.-518+89876C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,162 control chromosomes in the GnomAD database, including 30,917 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 0.59 (30917 hom., cov: 33)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

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]

C2orf88 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf88	XM_047446008.1	c.-518+89876C>T		intron_variant			XP_047301964.1
C2orf88	XM_047446009.1	c.-517-92515C>T		intron_variant			XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000478197.1	n.220-91784C>T		intron_variant		4
C2orf88	ENST00000495546.1	n.202-92515C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90211 AN: 152044 Hom.: 30921 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.593 AC: 90210 AN: 152162 Hom.: 30917 Cov.: 33 AF XY: 0.600 AC XY: 44601 AN XY: 74372

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.625

Alfa AF: 0.544 Hom.: 1973

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7575810; hg19: chr2-190852165;