19-17406017-AGGGCCTGGGTCTGGGGGCG-AGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTGGGGGCG

Position:

• chr19-17406017-AGGGCCTGGGTCTGGGGGCG-AGGGCCTGGGTCTGGGGGCGGGGCCTGGGTCTGGGGGCG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NR_130765.1(BISPR):​n.310+36_311-28dup 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 0.18 (2472 hom., cov: 29)
  • Exomes 𝑓: 0.017 (6 hom.)
  • 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 Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0167 (55/3296) while in subpopulation SAS AF= 0.0611 (37/606). AF 95% confidence interval is 0.0455. There are 6 homozygotes in gnomad4_exome. There are 36 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BISPR	NR_130765.1	n.310+36_311-28dup		intron_variant, non_coding_transcript_variant
MVB12A	NM_001304547.2	c.-406-46_-406-28dup		intron_variant			NP_001291476.1
BISPR	NR_130766.1	n.87-46_87-28dup		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_226-28dup		intron_variant, non_coding_transcript_variant		1
MVB12A	ENST00000528604.5	c.-224-46_-224-28dup		intron_variant		3		ENSP00000435052
MVB12A	ENST00000528911.5	c.-406-46_-406-28dup		intron_variant		5		ENSP00000433280

Frequencies

GnomAD3 genomes AF: 0.00 AC: 25973 AN: 147042 Hom.: 2470 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0633

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.0167 AC: 55 AN: 3296 Hom.: 6 Cov.: 0 AF XY: 0.0187 AC XY: 36 AN XY: 1924

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00746

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0611

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00587

Gnomad4 OTH exome AF: 0.0238

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.177 AC: 26015 AN: 147162 Hom.: 2472 Cov.: 29 AF XY: 0.179 AC XY: 12770 AN XY: 71528

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.190

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;