2-189940936-A-G

Variant names:

• chr2-189940936-A-G
• rs7571613
• XM_047446008.1:c.-518+43373A>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+61109A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,136 control chromosomes in the GnomAD database, including 3,096 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 0.20 (3096 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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+61109A>G		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.201+61109A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30019 AN: 152018 Hom.: 3093 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.198 AC: 30055 AN: 152136 Hom.: 3096 Cov.: 32 AF XY: 0.194 AC XY: 14467 AN XY: 74400

African (AFR) AF: 0.267 AC: 11076 AN: 41480

American (AMR) AF: 0.147 AC: 2244 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3466

East Asian (EAS) AF: 0.106 AC: 547 AN: 5174

South Asian (SAS) AF: 0.160 AC: 771 AN: 4830

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12354 AN: 67996

Other (OTH) AF: 0.206 AC: 436 AN: 2116

Alfa AF: 0.187 Hom.: 10883

Bravo AF: 0.201

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		0.22

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: rs7571613;

hg19: chr2-190805662;