9-35561994-G-GCTTA

Variant names:

• chr9-35561994-G-GCTTA
• rs1822209511
• NM_001164310.3:c.*12_*13insTAAG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001287239.2(CIMIP2B):​c.794_795insTAAG​(p.Phe267GlnfsTer37) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 29)
• Consequence: CIMIP2B NM_001287239.2 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.175

Genes affected

CIMIP2B (HGNC:34242): (ciliary microtubule inner protein 2B)

RUSC2 (HGNC:23625): (RUN and SH3 domain containing 2) This gene encodes a RUN and SH3 domain containing protein that interacts with Rab1b and Rab1-binding protein GM130. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jun 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMIP2B	NM_001164310.3	c.*12_*13insTAAG		3_prime_UTR_variant	Exon 6 of 6	ENST00000399742.7	NP_001157782.1
RUSC2	NM_014806.5	c.*612_*613insCTTA		downstream_gene_variant		ENST00000361226.8	NP_055621.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM166B	ENST00000399742	c.*12_*13insTAAG		3_prime_UTR_variant	Exon 6 of 6	1	NM_001164310.3	ENSP00000382646.2
RUSC2	ENST00000361226.8	c.*612_*613insCTTA		downstream_gene_variant		2	NM_014806.5	ENSP00000355177.3

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 29

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Meckel-Gruber syndrome Uncertain:1

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Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1822209511; hg19: chr9-35561991;