19-17406017-AGGGCCTGGGTCTGGGGGCG-A

Position:

• chr19-17406017-AGGGCCTGGGTCTGGGGGCG-A

Variant summary

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

The NR_130765.1(BISPR):​n.310+36_311-28del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000257 in 147,822 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00026 (0 hom., cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BISPR NR_130765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BISPR	NR_130765.1	n.310+36_311-28del		intron_variant, non_coding_transcript_variant
MVB12A	NM_001304547.2	c.-406-46_-406-28del		intron_variant			NP_001291476.1
BISPR	NR_130766.1	n.87-46_87-28del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BISPR	ENST00000635435.2	n.225+44_226-28del		intron_variant, non_coding_transcript_variant		1
MVB12A	ENST00000528604.5	c.-224-46_-224-28del		intron_variant		3		ENSP00000435052
MVB12A	ENST00000528911.5	c.-406-46_-406-28del		intron_variant		5		ENSP00000433280

Frequencies

GnomAD3 genomes AF: 0.000257 AC: 38 AN: 147822 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000877

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00129

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000253

Gnomad OTH AF: 0.000499

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3296 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1924

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000257 AC: 38 AN: 147822 Hom.: 0 Cov.: 29 AF XY: 0.000292 AC XY: 21 AN XY: 71818

Gnomad4 AFR AF: 0.000101

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000877

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00129

Gnomad4 NFE AF: 0.000253

Gnomad4 OTH AF: 0.000499

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;