rs11894651

Variant names:

• chr2-97701308-C-A
• rs11894651
• NM_001351368.2:c.665+4C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-97701308-C-A
• chr2-97701308-C-G
• chr2-97701308-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C2orf92	NM_001351368.2	c.665+4C>A		splice_region_variant, intron_variant	Intron 7 of 7	ENST00000627399.4	NP_001338297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf92	ENST00000627399.4	c.665+4C>A		splice_region_variant, intron_variant	Intron 7 of 7	5	NM_001351368.2	ENSP00000490587.1

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

African (AFR) AF: 0.708 AC: 5078 AN: 7176

American (AMR) AF: 0.514 AC: 3820 AN: 7432

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 5740 AN: 9240

East Asian (EAS) AF: 0.385 AC: 8820 AN: 22890

South Asian (SAS) AF: 0.258 AC: 782 AN: 3030

European-Finnish (FIN) AF: 0.774 AC: 16431 AN: 21220

Middle Eastern (MID) AF: 0.594 AC: 769 AN: 1294

European-Non Finnish (NFE) AF: 0.729 AC: 115197 AN: 157954

Other (OTH) AF: 0.667 AC: 10919 AN: 16364

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

African (AFR) AF: 0.702 AC: 29105 AN: 41486

American (AMR) AF: 0.576 AC: 8809 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2007 AN: 5158

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4814

European-Finnish (FIN) AF: 0.773 AC: 8172 AN: 10572

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49901 AN: 67978

Other (OTH) AF: 0.682 AC: 1437 AN: 2108

Alfa AF: 0.699 Hom.: 63261

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
PhyloP100		2.0

Splicing

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

Other links and lift over

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