2-189937527-G-C

Variant names:

• chr2-189937527-G-C
• rs11895934
• ENST00000478197.1:n.219+57700G>C

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+57700G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,786 control chromosomes in the GnomAD database, including 3,396 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 0.20 (3396 hom., cov: 31)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000478197.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf88	ENST00000478197.1	TSL:4	n.219+57700G>C		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.201+57700G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30984 AN: 151666 Hom.: 3392 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.204 AC: 31020 AN: 151786 Hom.: 3396 Cov.: 31 AF XY: 0.201 AC XY: 14913 AN XY: 74178

African (AFR) AF: 0.292 AC: 12078 AN: 41362

American (AMR) AF: 0.149 AC: 2280 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.106 AC: 549 AN: 5162

South Asian (SAS) AF: 0.157 AC: 752 AN: 4790

European-Finnish (FIN) AF: 0.158 AC: 1658 AN: 10508

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12288 AN: 67926

Other (OTH) AF: 0.211 AC: 445 AN: 2108

Alfa AF: 0.0943 Hom.: 144

Bravo AF: 0.208

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.53
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs11895934; hg19: chr2-190802253;