rs16832404

chr2-190188403-T-Cchr2-190188403-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042519.2(C2orf88):c.-165+7294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,272 control chromosomes in the GnomAD database, including 1,171 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 0.12 (1171 hom., cov: 32)
• Consequence: C2orf88 NM_001042519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	NM_001042519.2	c.-165+7294T>C		intron_variant		ENST00000340623.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000340623.4	c.-165+7294T>C		intron_variant		1	NM_001042519.2	P1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18012 AN: 152154 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 18031 AN: 152272 Hom.: 1171 Cov.: 32 AF XY: 0.118 AC XY: 8805 AN XY: 74448

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0816

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.0994

Gnomad4 OTH AF: 0.119

Alfa AF: 0.101 Hom.: 1464

Bravo AF: 0.123

Asia WGS AF: 0.188 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	15
Dann	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832404; hg19: chr2-191053129;