rs13401889

Positions:

• chr2-190045833-T-C

Variant summary

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

The XM_047446008.1(C2orf88):​c.-517-34121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,016 control chromosomes in the GnomAD database, including 8,433 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 0.30 (8433 hom., cov: 32)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-517-34121T>C		intron_variant
C2orf88	XM_047446009.1	c.-517-34121T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000478197.1	n.220-33390T>C		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.202-34121T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45036 AN: 151898 Hom.: 8410 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.297 AC: 45117 AN: 152016 Hom.: 8433 Cov.: 32 AF XY: 0.290 AC XY: 21538 AN XY: 74304

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.301

Alfa AF: 0.261 Hom.: 812

Bravo AF: 0.318

Asia WGS AF: 0.242 AC: 840 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	2.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13401889; hg19: chr2-190910559;