7-150792155-AC-GA

Variant names:

• chr7-150792155-AC-GA
• NM_001101312.2:c.620_621delGTinsTC
• TMEM176B p.Arg207Leu

Variant summary

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

The NM_001101312.2(TMEM176B):​c.620_621delGTinsTC​(p.Arg207Leu) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R207H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TMEM176B NM_001101312.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 0 publications found

Genes affected

TMEM176B (HGNC:29596): (transmembrane protein 176B) Predicted to be involved in negative regulation of dendritic cell differentiation. Predicted to be located in nuclear membrane. 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_001101312.2. 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
	TMEM176B	NM_001101312.2	MANE Select	c.620_621delGTinsTC	p.Arg207Leu	missense	N/A	NP_001094782.1	Q3YBM2-1
	TMEM176B	NM_001362691.2		c.668_669delGTinsTC	p.Arg223Leu	missense	N/A	NP_001349620.1
	TMEM176B	NM_001362692.2		c.668_669delGTinsTC	p.Arg223Leu	missense	N/A	NP_001349621.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM176B	ENST00000326442.10	TSL:1 MANE Select	c.620_621delGTinsTC	p.Arg207Leu	missense	N/A	ENSP00000318409.5	Q3YBM2-1
	TMEM176B	ENST00000447204.6	TSL:1	c.620_621delGTinsTC	p.Arg207Leu	missense	N/A	ENSP00000410269.2	Q3YBM2-1
	TMEM176B	ENST00000854817.1		c.764_765delGTinsTC	p.Arg255Leu	missense	N/A	ENSP00000524876.1

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		0.37

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: chr7-150489243;