Variant chr19-17406017-A-AGGGCCTGAGTCTGGGGGCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NR_130765.1(BISPR):n.310+29_310+30insAGTCTGGGGGCGGGGCCTG 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 0.000946 in 151,232 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.00089 ( 2 hom., cov: 29)

Exomes 𝑓: 0.0033 ( 2 hom. )

Consequence

BISPR
NR_130765.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.137

Variant links:

Genes affected

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

BISPR links:

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]

MVB12A links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000892 (132/147936) while in subpopulation SAS AF= 0.0284 (129/4538). AF 95% confidence interval is 0.0244. There are 2 homozygotes in gnomad4. There are 99 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
BISPR	NR_130765.1 linkuse as main transcript	n.310+29_310+30insAGTCTGGGGGCGGGGCCTG	intron_variant, non_coding_transcript_variant
MVB12A	NM_001304547.2 linkuse as main transcript	c.-406-53_-406-52insAGTCTGGGGGCGGGGCCTG	intron_variant	NP_001291476.1
BISPR	NR_130766.1 linkuse as main transcript	n.87-53_87-52insAGTCTGGGGGCGGGGCCTG	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein
BISPR	ENST00000635435.2 linkuse as main transcript	n.225+37_225+38insAGTCTGGGGGCGGGGCCTG	intron_variant, non_coding_transcript_variant	1
MVB12A	ENST00000528604.5 linkuse as main transcript	c.-224-53_-224-52insAGTCTGGGGGCGGGGCCTG	intron_variant	3	ENSP00000435052
MVB12A	ENST00000528911.5 linkuse as main transcript	c.-406-53_-406-52insAGTCTGGGGGCGGGGCCTG	intron_variant	5	ENSP00000433280

Frequencies

GnomAD3 genomes

AF:

0.000879

AC:

130

AN:

147820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000760

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0280

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00334

AC:

AN:

3296

Hom.:

Cov.:

AF XY:

0.00520

AC XY:

AN XY:

1924

show subpopulations

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:

0.0182

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.000892

AC:

132

AN:

147936

Hom.:

Cov.:

AF XY:

0.00138

AC XY:

AN XY:

71944

show subpopulations

Gnomad4 AFR

AF:

0.0000758

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0284

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000169

Hom.:

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Human immunodeficiency virus type 1, rapid progression to AIDS

Other:1

association, no assertion criteria provided

research

National AIDS Research Institute, National AIDS Research Institute

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over