1-230843669-C-T

Variant names:

• chr1-230843669-C-T
• rs150339183
• NM_032800.3:c.612G>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_032800.3(C1orf198):​c.612G>A​(p.Glu204Glu) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C1orf198 NM_032800.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 0 publications found

Genes affected

C1orf198 (HGNC:25900): (chromosome 1 open reading frame 198) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BP7: Synonymous conserved (PhyloP=0.649 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032800.3. 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
	C1orf198	NM_032800.3	MANE Select	c.612G>A	p.Glu204Glu	synonymous	Exon 3 of 4	NP_116189.1	Q9H425-1
	C1orf198	NM_001136494.2		c.498G>A	p.Glu166Glu	synonymous	Exon 5 of 6	NP_001129966.1	Q9H425-3
	C1orf198	NM_001136495.2		c.222G>A	p.Glu74Glu	synonymous	Exon 3 of 4	NP_001129967.1	Q9H425-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf198	ENST00000366663.10	TSL:1 MANE Select	c.612G>A	p.Glu204Glu	synonymous	Exon 3 of 4	ENSP00000355623.5	Q9H425-1
	C1orf198	ENST00000470540.5	TSL:2	c.498G>A	p.Glu166Glu	synonymous	Exon 5 of 6	ENSP00000428172.1	Q9H425-3
	C1orf198	ENST00000523410.1	TSL:2	c.222G>A	p.Glu74Glu	synonymous	Exon 3 of 4	ENSP00000430967.1	Q9H425-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	8.2
DANN	Benign	0.50
PhyloP100		0.65
Mutation Taster		=287/13	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: rs150339183; hg19: chr1-230979415;