rs11894651

chr2-97701308-C-Achr2-97701308-C-T

Variant summary

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

The NM_001351368.2(C2orf92):c.665+4C>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 398,672 control chromosomes in the GnomAD database, including 95,255 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 0.68 (36398 hom., cov: 32)
  • Exomes 𝑓: 0.68 (58857 hom.)
• Consequence: C2orf92 NM_001351368.2 splice_donor_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00

Genes affected

C2orf92 (HGNC:49272): (chromosome 2 open reading frame 92) 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=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf92	NM_001351368.2	c.665+4C>A		splice_donor_region_variant, intron_variant		ENST00000627399.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf92	ENST00000627399.4	c.665+4C>A		splice_donor_region_variant, intron_variant		5	NM_001351368.2	A2

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103751 AN: 151954 Hom.: 36376 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.683

GnomAD4 exome AF: 0.679 AC: 167556 AN: 246600 Hom.: 58857 Cov.: 0 AF XY: 0.679 AC XY: 84933 AN XY: 125000

Gnomad4 AFR exome AF: 0.708

Gnomad4 AMR exome AF: 0.514

Gnomad4 ASJ exome AF: 0.621

Gnomad4 EAS exome AF: 0.385

Gnomad4 SAS exome AF: 0.258

Gnomad4 FIN exome AF: 0.774

Gnomad4 NFE exome AF: 0.729

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.683 AC: 103821 AN: 152072 Hom.: 36398 Cov.: 32 AF XY: 0.675 AC XY: 50140 AN XY: 74314

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.682

Alfa AF: 0.661 Hom.: 9616

Bravo AF: 0.674

Asia WGS AF: 0.396 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	15
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11894651; hg19: chr2-98317771; COSMIC: COSV71377080; COSMIC: COSV71377080;