20-35652944-TCC-CCG

Variant names:

• chr20-35652944-TCC-CCG
• NM_006047.6:c.2377_2379delGGAinsCGG
• RBM12 p.Gly793Arg

Variant summary

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

The NM_006047.6(RBM12):​c.2377_2379delGGAinsCGG​(p.Gly793Arg) 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: 32)
• Consequence: RBM12 NM_006047.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.09
• Publications: 0 publications found

Genes affected

RBM12 (HGNC:9898): (RNA binding motif protein 12) This gene encodes a protein that contains several RNA-binding motifs, potential transmembrane domains, and proline-rich regions. This gene and the gene for copine I overlap at map location 20q11.21. Alternative splicing in the 5' UTR results in four transcript variants. All variants encode the same protein. [provided by RefSeq, Nov 2010]

CPNE1 (HGNC:2314): (copine 1) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a calcium-dependent protein that also contains two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. However, the encoded protein does not contain a predicted signal sequence or transmembrane domains. This protein has a broad tissue distribution and it may function in membrane trafficking. This gene and the gene for RNA binding motif protein 12 overlap at map location 20q11.21. Alternate splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Aug 2008]

ENSG00000272897 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006047.6. 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
	RBM12	NM_006047.6	MANE Select	c.2377_2379delGGAinsCGG	p.Gly793Arg	missense	N/A	NP_006038.2
	CPNE1	NM_152925.3	MANE Select	c.-1+11814_-1+11816delGGAinsCGG		intron	N/A	NP_690902.1	Q99829
	RBM12	NM_001198838.2		c.2377_2379delGGAinsCGG	p.Gly793Arg	missense	N/A	NP_001185767.1	Q9NTZ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM12	ENST00000374114.8	TSL:1 MANE Select	c.2377_2379delGGAinsCGG	p.Gly793Arg	missense	N/A	ENSP00000363228.3	Q9NTZ6
	RBM12	ENST00000359646.1	TSL:1	c.2377_2379delGGAinsCGG	p.Gly793Arg	missense	N/A	ENSP00000352668.1	Q9NTZ6
	RBM12	ENST00000374104.7	TSL:1	c.2377_2379delGGAinsCGG	p.Gly793Arg	missense	N/A	ENSP00000363217.3	Q9NTZ6

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		7.1

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: chr20-34240866;