C22orf42 p.Gly95Arg

Variant names:

• chr22-32154268-C-G
• NM_001010859.3:c.283G>C
• C22orf42 p.Gly95Arg

Your query was ambiguous. Multiple possible variants found:

• chr22-32154268-C-G
• chr22-32154268-C-T
• chr22-32154266-CCC-ACG
• chr22-32154266-CCC-GCG
• chr22-32154266-CCC-TCG
• chr22-32154266-CCC-TCT

Variant summary

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

The NM_001010859.3(C22orf42):​c.283G>C​(p.Gly95Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C22orf42 NM_001010859.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 0 publications found

Genes affected

C22orf42 (HGNC:27160): (chromosome 22 open reading frame 42)

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 (MetaRNN=0.13698468).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010859.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C22orf42	NM_001010859.3	MANE Select	c.283G>C	p.Gly95Arg	missense	Exon 2 of 9	NP_001010859.1	Q6IC83

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C22orf42	ENST00000382097.4	TSL:1 MANE Select	c.283G>C	p.Gly95Arg	missense	Exon 2 of 9	ENSP00000371529.3	Q6IC83
	C22orf42	ENST00000467813.1	TSL:2	n.390G>C		non_coding_transcript_exon	Exon 2 of 8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.44
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	5.9
DANN	Benign	0.73
DEOGEN2	Benign	0.0039	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0022	N
M_CAP	Benign	0.0048	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.21
PROVEAN	Benign	0.040	N
REVEL	Benign	0.052
Sift	Benign	0.11	T
Sift4G	Benign	0.20	T
Varity_R		0.067
gMVP		0.068
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr22-32550255;