2-189962297-A-G

Variant names:

• chr2-189962297-A-G
• rs2053163
• ENST00000478197.1:n.219+82470A>G

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+82470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,072 control chromosomes in the GnomAD database, including 25,091 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 0.52 (25091 hom., cov: 31)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_047446008.1	c.-518+64734A>G		intron_variant	Intron 2 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-518+82619A>G		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.219+82470A>G		intron_variant	Intron 1 of 1	4
C2orf88	ENST00000495546.1	n.201+82470A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78978 AN: 151956 Hom.: 25100 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.519 AC: 78966 AN: 152072 Hom.: 25091 Cov.: 31 AF XY: 0.522 AC XY: 38819 AN XY: 74338

African (AFR) AF: 0.146 AC: 6050 AN: 41516

American (AMR) AF: 0.579 AC: 8846 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1575 AN: 5164

South Asian (SAS) AF: 0.695 AC: 3344 AN: 4810

European-Finnish (FIN) AF: 0.695 AC: 7341 AN: 10558

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.700 AC: 47604 AN: 67968

Other (OTH) AF: 0.547 AC: 1156 AN: 2112

Alfa AF: 0.637 Hom.: 98695

Bravo AF: 0.489

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2053163; hg19: chr2-190827023;