rs288817

Variant names:

• chr2-189962255-G-A
• rs288817
• XM_047446008.1:c.-518+64692G>A

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+82428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,196 control chromosomes in the GnomAD database, including 1,483 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 0.083 (1483 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 0 publications found

Genes affected

AKAP19 (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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000478197.1. 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	ENST00000478197.1	TSL:4	n.219+82428G>A		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.201+82428G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12614 AN: 152078 Hom.: 1473 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00148

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152196 Hom.: 1483 Cov.: 32 AF XY: 0.0819 AC XY: 6092 AN XY: 74406

African (AFR) AF: 0.253 AC: 10486 AN: 41492

American (AMR) AF: 0.0648 AC: 992 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3468

East Asian (EAS) AF: 0.165 AC: 854 AN: 5174

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4824

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00150 AC: 102 AN: 68018

Other (OTH) AF: 0.0673 AC: 142 AN: 2110

Alfa AF: 0.0380 Hom.: 1261

Bravo AF: 0.0991

Asia WGS AF: 0.0650 AC: 227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs288817; hg19: chr2-190826981;