rs13034723

Variant names:

• chr2-190120954-G-A
• rs13034723
• ENST00000450357.5:c.-290+29984G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-190120954-G-A
• chr2-190120954-G-C

Variant summary

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

The ENST00000450357.5(C2orf88):​c.-290+29984G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,912 control chromosomes in the GnomAD database, including 13,181 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 0.38 (13181 hom., cov: 31)
• Consequence: C2orf88 ENST00000450357.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 14 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_011511983.2	c.-290+25352G>A		intron_variant	Intron 3 of 4		XP_011510285.1
AKAP19	XM_047446008.1	c.-290+25352G>A		intron_variant	Intron 5 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-290+25352G>A		intron_variant	Intron 4 of 5		XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000450357.5	c.-290+29984G>A		intron_variant	Intron 2 of 3	3		ENSP00000394370.1
C2orf88	ENST00000490033.5	n.226+25352G>A		intron_variant	Intron 3 of 4	3
C2orf88	ENST00000495546.1	n.271+40931G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57595 AN: 151792 Hom.: 13184 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.379 AC: 57590 AN: 151912 Hom.: 13181 Cov.: 31 AF XY: 0.392 AC XY: 29077 AN XY: 74240

African (AFR) AF: 0.128 AC: 5305 AN: 41462

American (AMR) AF: 0.424 AC: 6468 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.674 AC: 3481 AN: 5164

South Asian (SAS) AF: 0.672 AC: 3242 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6362 AN: 10510

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30187 AN: 67928

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.421 Hom.: 47407

Bravo AF: 0.351

Asia WGS AF: 0.605 AC: 2102 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.60
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs13034723; hg19: chr2-190985680;