Variant rs11894651 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001351368.2(C2orf92):c.665+4C>A variant causes a splice 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_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.00

Variant links:

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]

C2orf92 links:

C2orf92 (HGNC:):

C2orf92 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
C2orf92	NM_001351368.2 linkuse as main transcript	c.665+4C>A		splice_region_variant, intron_variant		ENST00000627399.4	NP_001338297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf92	ENST00000627399.4 linkuse as main transcript	c.665+4C>A		splice_region_variant, intron_variant		5	NM_001351368.2	ENSP00000490587.1		A0A1B0GVN3

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

103751

AN:

151954

Hom.:

36376

Cov.:

show subpopulations

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.:

AF XY:

0.679

AC XY:

84933

AN XY:

125000

show subpopulations

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.:

AF XY:

0.675

AC XY:

50140

AN XY:

74314

show subpopulations

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

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over