1-34197629-A-G

Variant names:

• chr1-34197629-A-G
• rs201420557
• NM_001134734.2:c.725A>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001134734.2(C1orf94):​c.725A>G​(p.Gln242Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q242L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: C1orf94 NM_001134734.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.67
• Publications: 0 publications found

Genes affected

C1orf94 (HGNC:28250): (chromosome 1 open reading frame 94)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.37188894).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134734.2. 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
	C1orf94	NM_001134734.2	MANE Select	c.725A>G	p.Gln242Arg	missense	Exon 2 of 7	NP_001128206.1	Q6P1W5-1
	C1orf94	NM_032884.5		c.155A>G	p.Gln52Arg	missense	Exon 2 of 7	NP_116273.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf94	ENST00000488417.2	TSL:1 MANE Select	c.725A>G	p.Gln242Arg	missense	Exon 2 of 7	ENSP00000435634.1	Q6P1W5-1
	C1orf94	ENST00000373374.7	TSL:1	c.155A>G	p.Gln52Arg	missense	Exon 2 of 7	ENSP00000362472.3	Q6P1W5-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.077	T
BayesDel_noAF	Benign	-0.35
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.040	T
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.37	T
MetaSVM	Benign	-0.64	T
MutationAssessor	Benign	1.7	L
PhyloP100		3.7
PROVEAN	Uncertain	-2.9	D
REVEL	Benign	0.096
Sift	Uncertain	0.011	D
Sift4G	Uncertain	0.010	D
Polyphen		0.99	D
Vest4		0.61
MutPred		0.17		Gain of MoRF binding (P = 0.0243)
MVP		0.39
MPC		0.26
ClinPred		0.97	D
GERP RS		5.0
Varity_R		0.25
gMVP		0.14
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs201420557; hg19: chr1-34663230;