19-38407003-CGA-GGT

Variant names:

• chr19-38407003-CGA-GGT
• NM_174905.4:c.844_846delCGAinsGGT
• FAM98C p.Arg282Gly

Variant summary

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

The NM_174905.4(FAM98C):​c.844_846delCGAinsGGT​(p.Arg282Gly) variant causes a missense change. 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: 31)
• Consequence: FAM98C NM_174905.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.32
• Publications: 0 publications found

Genes affected

FAM98C (HGNC:27119): (family with sequence similarity 98 member C) Predicted to be part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174905.4. 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
	FAM98C	NM_174905.4	MANE Select	c.844_846delCGAinsGGT	p.Arg282Gly	missense	N/A	NP_777565.3
	FAM98C	NM_001351675.1		c.672+1368_672+1370delCGAinsGGT		intron	N/A	NP_001338604.1	Q17RN3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM98C	ENST00000252530.10	TSL:1 MANE Select	c.844_846delCGAinsGGT	p.Arg282Gly	missense	N/A	ENSP00000252530.4	Q17RN3-1
	FAM98C	ENST00000588262.5	TSL:1	c.443_445delCGAinsGGT	p.ProSer148ArgCys	missense	N/A	ENSP00000467974.1	K7EQT7
	FAM98C	ENST00000343358.11	TSL:1	c.672+1368_672+1370delCGAinsGGT		intron	N/A	ENSP00000340348.6	Q17RN3-2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.3

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: chr19-38897643;