chr2-189947246-T-C

Position:

• chr2-189947246-T-C

Variant summary

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

The XM_047446008.1(C2orf88):​c.-518+49683T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,156 control chromosomes in the GnomAD database, including 2,465 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 0.18 (2465 hom., cov: 33)
• Consequence: C2orf88 XM_047446008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf88	XM_047446008.1	c.-518+49683T>C		intron_variant			XP_047301964.1
C2orf88	XM_047446009.1	c.-518+67568T>C		intron_variant			XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000478197.1	n.219+67419T>C		intron_variant, non_coding_transcript_variant		4
C2orf88	ENST00000495546.1	n.201+67419T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27029 AN: 152038 Hom.: 2463 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.178 AC: 27050 AN: 152156 Hom.: 2465 Cov.: 33 AF XY: 0.175 AC XY: 13039 AN XY: 74390

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.192

Alfa AF: 0.182 Hom.: 492

Bravo AF: 0.178

Asia WGS AF: 0.166 AC: 579 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7564968; hg19: chr2-190811972;