chrX-102154299-C-CAGAG

Variant names:

• chrX-102154299-C-CAGAG
• NM_001012978.3:c.-35_-34insCTCT

Variant summary

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

The NM_001012978.3(BEX5):​c.-35_-34insCTCT variant causes a splice region change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 20)
• Consequence: BEX5 NM_001012978.3 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

Genes affected

BEX5 (HGNC:27990): (brain expressed X-linked 5) Predicted to enable signaling receptor binding activity. Predicted to be involved in signal transduction. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BEX5	NM_001012978.3	c.-35_-34insCTCT		splice_region_variant	Exon 3 of 3	ENST00000333643.4	NP_001012996.1
BEX5	NM_001012978.3	c.-35_-34insCTCT		5_prime_UTR_variant	Exon 3 of 3	ENST00000333643.4	NP_001012996.1
BEX5	NM_001159560.2	c.-35_-34insCTCT		splice_region_variant	Exon 3 of 3		NP_001153032.1
BEX5	NM_001159560.2	c.-35_-34insCTCT		5_prime_UTR_variant	Exon 3 of 3		NP_001153032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BEX5	ENST00000333643.4	c.-35_-34insCTCT		splice_region_variant	Exon 3 of 3	1	NM_001012978.3	ENSP00000328030.3
BEX5	ENST00000333643.4	c.-35_-34insCTCT		5_prime_UTR_variant	Exon 3 of 3	1	NM_001012978.3	ENSP00000328030.3
BEX5	ENST00000543160.5	c.-35_-34insCTCT		splice_region_variant	Exon 3 of 3	3		ENSP00000446054.1
BEX5	ENST00000543160.5	c.-35_-34insCTCT		5_prime_UTR_variant	Exon 3 of 3	3		ENSP00000446054.1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome Cov.: 19

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-101409271;