NM_001351368.2:c.665+4C>T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001351368.2(C2orf92):​c.665+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000405 in 246,668 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000041 (0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351368.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf92	NM_001351368.2	MANE Select	c.665+4C>T		splice_region intron	N/A	NP_001338297.1
	C2orf92	NM_001410919.1		c.563+4C>T		splice_region intron	N/A	NP_001397848.1
	C2orf92	NR_038386.2		n.1001+4C>T		splice_region intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf92	ENST00000627399.4	TSL:5 MANE Select	c.665+4C>T		splice_region intron	N/A	ENSP00000490587.1
	C2orf92	ENST00000451384.6	TSL:1	n.968+4C>T		splice_region intron	N/A
	C2orf92	ENST00000599501.6	TSL:5	c.563+4C>T		splice_region intron	N/A	ENSP00000490827.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000405 AC: 1 AN: 246668 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 125032

African (AFR) AF: 0.00 AC: 0 AN: 7178

American (AMR) AF: 0.00 AC: 0 AN: 7432

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9240

East Asian (EAS) AF: 0.0000437 AC: 1 AN: 22894

South Asian (SAS) AF: 0.00 AC: 0 AN: 3030

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21232

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 157998

Other (OTH) AF: 0.00 AC: 0 AN: 16370

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 63261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.69
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;