1-172468452-GC-CG

Variant names:

• chr1-172468452-GC-CG
• NM_139240.4:c.410_411delGCinsCG
• C1orf105 p.Ser137Thr

Variant summary

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

The NM_139240.4(C1orf105):​c.410_411delGCinsCG​(p.Ser137Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C1orf105 NM_139240.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 0 publications found

Genes affected

C1orf105 (HGNC:29591): (chromosome 1 open reading frame 105)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139240.4. 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
	C1orf105	NM_139240.4	MANE Select	c.410_411delGCinsCG	p.Ser137Thr	missense	N/A	NP_640333.3
	C1orf105	NM_001300760.1		c.380_381delGCinsCG	p.Ser127Thr	missense	N/A	NP_001287689.1	Q5R3C7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf105	ENST00000367727.9	TSL:1 MANE Select	c.410_411delGCinsCG	p.Ser137Thr	missense	N/A	ENSP00000356700.4	O95561
	C1orf105	ENST00000367725.4	TSL:2	c.380_381delGCinsCG	p.Ser127Thr	missense	N/A	ENSP00000356698.4	Q5R3C7
	C1orf105	ENST00000367726.1	TSL:3	n.214_215delGCinsCG		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.0030

Splicing

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: chr1-172437592;