11-62789092-CGT-GGC

Variant names:

• chr11-62789092-CGT-GGC
• NM_199337.3:c.166_168delCGTinsGGC
• TMEM179B p.Arg56Gly

Variant summary

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

The NM_199337.3(TMEM179B):​c.166_168delCGTinsGGC​(p.Arg56Gly) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R56C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TMEM179B NM_199337.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 0 publications found

Genes affected

TMEM179B (HGNC:33744): (transmembrane protein 179B) Located in nuclear speck and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

TMEM223 (HGNC:28464): (transmembrane protein 223) Predicted to be involved in nervous system development. Predicted to be integral component of membrane. [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_199337.3. 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
	TMEM179B	NM_199337.3	MANE Select	c.166_168delCGTinsGGC	p.Arg56Gly	missense	N/A	NP_955369.1	Q7Z7N9
	TMEM179B	NM_001363600.1		c.166_168delCGTinsGGC	p.Arg56Gly	missense	N/A	NP_001350529.1
	TMEM179B	NM_001363599.1		c.166_168delCGTinsGGC	p.Arg56Gly	missense	N/A	NP_001350528.1	G3V185

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM179B	ENST00000333449.9	TSL:1 MANE Select	c.166_168delCGTinsGGC	p.Arg56Gly	missense	N/A	ENSP00000333697.3	Q7Z7N9
	TMEM223	ENST00000525631.1	TSL:1	c.317-1169_317-1167delACGinsGCC		intron	N/A	ENSP00000436670.1	G5EA27
	TMEM179B	ENST00000892244.1		c.202_204delCGTinsGGC	p.Arg68Gly	missense	N/A	ENSP00000562303.1

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		-0.74

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: chr11-62556564;