rs13034723

Variant names:

• chr2-190120954-G-A
• rs13034723
• ENST00000917871.1:c.-165+40931G>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450357.5. 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	ENST00000917871.1		c.-165+40931G>A		intron	N/A	ENSP00000587930.1
	C2orf88	ENST00000450357.5	TSL:3	c.-290+29984G>A		intron	N/A	ENSP00000394370.1	C9JS57
	C2orf88	ENST00000490033.5	TSL:3	n.226+25352G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13034723;

hg19: chr2-190985680;