2-189940936-A-G

Position:

• chr2-189940936-A-G

Variant summary

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

The XM_047446008.1(C2orf88):​c.-518+43373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,136 control chromosomes in the GnomAD database, including 3,096 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 (3096 hom., cov: 32)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf88	XM_047446008.1	c.-518+43373A>G		intron_variant
C2orf88	XM_047446009.1	c.-518+61258A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf88	ENST00000478197.1	n.219+61109A>G		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.201+61109A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30019 AN: 152018 Hom.: 3093 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.198 AC: 30055 AN: 152136 Hom.: 3096 Cov.: 32 AF XY: 0.194 AC XY: 14467 AN XY: 74400

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.206

Alfa AF: 0.183 Hom.: 5326

Bravo AF: 0.201

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7571613; hg19: chr2-190805662;