rs1474359

chr2-190068280-T-Cchr2-190068280-T-G

Variant summary

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

The XM_047446008.1(C2orf88):c.-517-11674T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,110 control chromosomes in the GnomAD database, including 31,666 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 0.60 (31666 hom., cov: 32)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-517-11674T>C		intron_variant
C2orf88	XM_047446009.1	c.-517-11674T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000478197.1	n.220-10943T>C		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.202-11674T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90697 AN: 151992 Hom.: 31671 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.596 AC: 90694 AN: 152110 Hom.: 31666 Cov.: 32 AF XY: 0.605 AC XY: 44974 AN XY: 74362

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.607

Alfa AF: 0.716 Hom.: 21648

Bravo AF: 0.569

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.5
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1474359; hg19: chr2-190933006;