chr5-138439133-C-CGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT

Variant names:

• chr5-138439133-C-CGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT
• NM_001271803.2:c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT

Variant summary

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

The NM_001271803.2(REEP2):​c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT variant causes a 5 prime UTR 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 INS_BIG, 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: 31)
• Consequence: REEP2 NM_001271803.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 0 publications found

Genes affected

REEP2 (HGNC:17975): (receptor accessory protein 2) This gene encodes a member of the receptor expression enhancing protein family. Studies of a related gene in mouse suggest that the encoded protein is found in the cell membrane and enhances the function of sweet taste receptors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

REEP2 Gene-Disease associations (from GenCC):

• hereditary spastic paraplegia 72

  Inheritance: AD, AR, SD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
• hereditary spastic paraplegia

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271803.2. 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
	REEP2	NM_001271803.2	MANE Select	c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		5_prime_UTR	Exon 1 of 8	NP_001258732.1	Q9BRK0-2
	REEP2	NM_016606.4		c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		5_prime_UTR	Exon 1 of 8	NP_057690.2
	REEP2	NR_073448.2		n.77_78insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		non_coding_transcript_exon	Exon 1 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REEP2	ENST00000378339.7	TSL:1 MANE Select	c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		5_prime_UTR	Exon 1 of 8	ENSP00000367590.2	Q9BRK0-2
	REEP2	ENST00000254901.9	TSL:1	c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		5_prime_UTR	Exon 1 of 8	ENSP00000254901.5	Q9BRK0-1
	REEP2	ENST00000903314.1		c.-76_-75insGTGCCATGGTGTCCTGGATCATCTCTCGCCTGGTGGT		5_prime_UTR	Exon 1 of 8	ENSP00000573373.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.44

Splicing

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

Other links and lift over

hg19: chr5-137774822;