19-17406017-A-AGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTGGGGGCG

Position:

• chr19-17406017-A-AGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTGGGGGCG

Variant summary

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

The NR_130765.1(BISPR):​n.311-28_311-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG variant causes a intron, non coding transcript 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: 𝑓 0.0000068 (0 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: BISPR NR_130765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

BISPR (HGNC:51290): (BST2 interferon stimulated positive regulator)

MVB12A (HGNC:25153): (multivesicular body subunit 12A) Enables lipid binding activity and ubiquitin binding activity. Involved in regulation of epidermal growth factor receptor signaling pathway; viral budding; and virus maturation. Located in several cellular components, including Golgi apparatus; centrosome; and nucleoplasm. Part of ESCRT I complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BISPR	NR_130765.1	n.311-28_311-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant, non_coding_transcript_variant
MVB12A	NM_001304547.2	c.-406-28_-406-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant			NP_001291476.1
BISPR	NR_130766.1	n.87-28_87-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BISPR	ENST00000635435.2	n.226-28_226-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant, non_coding_transcript_variant		1
MVB12A	ENST00000528604.5	c.-224-28_-224-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant		3		ENSP00000435052
MVB12A	ENST00000528911.5	c.-406-28_-406-27insGGGGCGGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTG		intron_variant		5		ENSP00000433280

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 147824 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000675

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000676 AC: 1 AN: 147824 Hom.: 0 Cov.: 29 AF XY: 0.0000139 AC XY: 1 AN XY: 71820

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000675

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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

LitVar

Other links and lift over

dbSNP: rs3217318; hg19: chr19-17516826;