rs998173

Variant names:

• chr2-190126900-A-T
• rs998173
• ENST00000450357.5:c.-290+35930A>T

Variant summary

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

The ENST00000450357.5(C2orf88):​c.-290+35930A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 152,148 control chromosomes in the GnomAD database, including 739 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 0.076 (739 hom., cov: 31)
• Consequence: C2orf88 ENST00000450357.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_011511983.2	c.-290+31298A>T		intron_variant	Intron 3 of 4		XP_011510285.1
AKAP19	XM_047446008.1	c.-290+31298A>T		intron_variant	Intron 5 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-290+31298A>T		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+35930A>T		intron_variant	Intron 2 of 3	3		ENSP00000394370.1
C2orf88	ENST00000490033.5	n.226+31298A>T		intron_variant	Intron 3 of 4	3
C2orf88	ENST00000495546.1	n.272-37036A>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11597 AN: 152030 Hom.: 734 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0777

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

GnomAD4 genome AF: 0.0764 AC: 11622 AN: 152148 Hom.: 739 Cov.: 31 AF XY: 0.0745 AC XY: 5540 AN XY: 74386

African (AFR) AF: 0.178 AC: 7389 AN: 41440

American (AMR) AF: 0.0502 AC: 768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.00787 AC: 38 AN: 4826

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0416 AC: 2830 AN: 68008

Other (OTH) AF: 0.0769 AC: 162 AN: 2108

Alfa AF: 0.0587 Hom.: 65

Bravo AF: 0.0824

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.81
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs998173; hg19: chr2-190991626;