ENST00000478197.1:n.219+36145A>G

Variant names:

• chr2-189915972-A-G
• rs12466395
• ENST00000478197.1:n.219+36145A>G

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000478197.1(C2orf88):​n.219+36145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,962 control chromosomes in the GnomAD database, including 35,040 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 0.66 (35040 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_047446008.1	c.-518+18409A>G		intron_variant	Intron 2 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-518+36294A>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+36145A>G		intron_variant	Intron 1 of 1	4
C2orf88	ENST00000495546.1	n.201+36145A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99599 AN: 151846 Hom.: 35030 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.656 AC: 99628 AN: 151962 Hom.: 35040 Cov.: 32 AF XY: 0.663 AC XY: 49217 AN XY: 74270

African (AFR) AF: 0.374 AC: 15514 AN: 41442

American (AMR) AF: 0.765 AC: 11680 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4594 AN: 5174

South Asian (SAS) AF: 0.783 AC: 3771 AN: 4814

European-Finnish (FIN) AF: 0.776 AC: 8175 AN: 10538

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51129 AN: 67936

Other (OTH) AF: 0.664 AC: 1404 AN: 2116

Alfa AF: 0.730 Hom.: 44740

Bravo AF: 0.644

Asia WGS AF: 0.765 AC: 2636 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12466395; hg19: chr2-190780698;