9-35102716-TC-CG

Variant names:

• chr9-35102716-TC-CG
• NM_013442.3:c.152_153delGAinsCG
• STOML2 p.Arg51Pro

Variant summary

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

The NM_013442.3(STOML2):​c.152_153delGAinsCG​(p.Arg51Pro) variant causes a missense change involving the alteration of a 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. R51Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: STOML2 NM_013442.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.45
• Publications: 0 publications found

Genes affected

STOML2 (HGNC:14559): (stomatin like 2) Enables GTPase binding activity and cardiolipin binding activity. Involved in several processes, including inorganic cation transmembrane transport; positive regulation of cardiolipin metabolic process; and positive regulation of mitochondrial DNA replication. Located in membrane raft; mitochondrial inner membrane; and mitochondrial intermembrane space. Is extrinsic component of plasma membrane. Colocalizes with several cellular components, including COP9 signalosome; T cell receptor complex; and immunological synapse. [provided by Alliance of Genome Resources, Apr 2022]

PIGO-AS1 (HGNC:55692): (PIGO antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013442.3. 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
	STOML2	NM_013442.3	MANE Select	c.152_153delGAinsCG	p.Arg51Pro	missense	N/A	NP_038470.1	Q9UJZ1-1
	STOML2	NM_001287031.2		c.152_153delGAinsCG	p.Arg51Pro	missense	N/A	NP_001273960.1	Q9UJZ1-2
	STOML2	NM_001287032.1		c.-2_-1delGAinsCG		5_prime_UTR	Exon 2 of 10	NP_001273961.1	Q9UJZ1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOML2	ENST00000356493.10	TSL:1 MANE Select	c.152_153delGAinsCG	p.Arg51Pro	missense	N/A	ENSP00000348886.5	Q9UJZ1-1
	STOML2	ENST00000940083.1		c.152_153delGAinsCG	p.Arg51Pro	missense	N/A	ENSP00000610142.1
	STOML2	ENST00000940081.1		c.152_153delGAinsCG	p.Arg51Pro	missense	N/A	ENSP00000610140.1

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		7.5

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: chr9-35102713;