rs10179572

chr2-227639787-A-G

Variant summary

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

The ENST00000509872.1(C2orf83):n.997+2297T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,878 control chromosomes in the GnomAD database, including 11,594 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 0.38 (11594 hom., cov: 31)
• Consequence: C2orf83 ENST00000509872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

C2orf83 (HGNC:25344): (chromosome 2 open reading frame 83) Predicted to enable vitamin transmembrane transporter activity. Predicted to be involved in vitamin transmembrane transport. Predicted to be integral component of 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf83	ENST00000509872.1	n.997+2297T>C		intron_variant, non_coding_transcript_variant
C2orf83	ENST00000641887.1	n.143+2436T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57771 AN: 151760 Hom.: 11581 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.381 AC: 57806 AN: 151878 Hom.: 11594 Cov.: 31 AF XY: 0.378 AC XY: 28088 AN XY: 74226

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.375

Alfa AF: 0.425 Hom.: 7371

Bravo AF: 0.367

Asia WGS AF: 0.313 AC: 1087 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.7
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10179572; hg19: chr2-228504503;