ENST00000917871.1:c.-235+103C>T

Variant names:

• chr2-189987439-C-T
• rs7575810
• ENST00000917871.1:c.-235+103C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000917871.1(C2orf88):​c.-235+103C>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 ENST00000917871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000917871.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf88	ENST00000917871.1		c.-235+103C>T		intron	N/A	ENSP00000587930.1
	C2orf88	ENST00000478197.1	TSL:4	n.220-91784C>T		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.202-92515C>T		intron	N/A

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

African (AFR) AF: 0.218 AC: 9061 AN: 41520

American (AMR) AF: 0.723 AC: 11041 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3470

East Asian (EAS) AF: 0.690 AC: 3564 AN: 5166

South Asian (SAS) AF: 0.781 AC: 3764 AN: 4820

European-Finnish (FIN) AF: 0.725 AC: 7677 AN: 10594

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50491 AN: 67998

Other (OTH) AF: 0.625 AC: 1319 AN: 2110

Alfa AF: 0.544 Hom.: 1973

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7575810;

hg19: chr2-190852165;