2-189987439-C-T

Variant names:

• chr2-189987439-C-T
• rs7575810
• ENST00000478197.1:n.220-91784C>T

Variant summary

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

The ENST00000478197.1(C2orf88):​n.220-91784C>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 ENST00000478197.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_047446008.1	c.-518+89876C>T		intron_variant	Intron 2 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-517-92515C>T		intron_variant	Intron 1 of 5		XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000478197.1	n.220-91784C>T		intron_variant	Intron 1 of 1	4
C2orf88	ENST00000495546.1	n.202-92515C>T		intron_variant	Intron 1 of 2	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

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 v4.3

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

Other links and lift over

dbSNP: rs7575810; hg19: chr2-190852165;