rs998173

Positions:

• chr2-190126900-A-T

Variant summary

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

The ENST00000450357.5(C2orf88):​c.-290+35930A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 152,148 control chromosomes in the GnomAD database, including 739 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 0.076 (739 hom., cov: 31)
• Consequence: C2orf88 ENST00000450357.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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 (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf88	XM_011511983.2	c.-290+31298A>T		intron_variant			XP_011510285.1
C2orf88	XM_047446008.1	c.-290+31298A>T		intron_variant			XP_047301964.1
C2orf88	XM_047446009.1	c.-290+31298A>T		intron_variant			XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000450357.5	c.-290+35930A>T		intron_variant		3		ENSP00000394370
C2orf88	ENST00000490033.5	n.226+31298A>T		intron_variant, non_coding_transcript_variant		3
C2orf88	ENST00000495546.1	n.272-37036A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11597 AN: 152030 Hom.: 734 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0777

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

GnomAD4 genome AF: 0.0764 AC: 11622 AN: 152148 Hom.: 739 Cov.: 31 AF XY: 0.0745 AC XY: 5540 AN XY: 74386

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.00787

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0587 Hom.: 65

Bravo AF: 0.0824

Asia WGS AF: 0.0200 AC: 69 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	3.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998173; hg19: chr2-190991626;