Genetic Variant ENST00000635435.2:n.225+44_226-28delGGGGCGGGGCCTGGGTCTG (chr19-17406017-AGGGCCTGGGTCTGGGGGCG-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The ENST00000635435.2(BISPR):n.225+44_226-28delGGGGCGGGGCCTGGGTCTG variant causes a intron 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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
ENST00000635435.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08

Publications

9 publications found

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 was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635435.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
MVB12A	NM_001304547.2	c.-406-46_-406-28delGGGGCGGGGCCTGGGTCTG	intron	N/A	NP_001291476.1
BISPR	NR_130765.1	n.310+36_311-28delGGGGCGGGGCCTGGGTCTG	intron	N/A
BISPR	NR_130766.1	n.87-46_87-28delGGGGCGGGGCCTGGGTCTG	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
BISPR	ENST00000635435.2	TSL:1	n.225+44_226-28delGGGGCGGGGCCTGGGTCTG	intron	N/A
BISPR	ENST00000634731.2	TSL:3	n.256_274delGGGGCGGGGCCTGGGTCTG	non_coding_transcript_exon	Exon 1 of 2
BISPR	ENST00000635572.1	TSL:4	n.291_309delGGGGCGGGGCCTGGGTCTG	non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.000257

AC:

AN:

147822

Hom.:

Cov.:

show subpopulations

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:

AN:

3296

Hom.:

AF XY:

0.00

AC XY:

AN XY:

1924

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

268

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

606

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

2044

Other (OTH)

AF:

0.00

AC:

AN:

168

GnomAD4 genome

AF:

0.000257

AC:

AN:

147822

Hom.:

Cov.:

AF XY:

0.000292

AC XY:

AN XY:

71818

show subpopulations

African (AFR)

AF:

0.000101

AC:

AN:

39468

American (AMR)

AF:

0.00

AC:

AN:

14812

Ashkenazi Jewish (ASJ)

AF:

0.000877

AC:

AN:

3422

East Asian (EAS)

AF:

0.00

AC:

AN:

5032

South Asian (SAS)

AF:

0.00

AC:

AN:

4546

European-Finnish (FIN)

AF:

0.00129

AC:

AN:

10104

Middle Eastern (MID)

AF:

0.00

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.000253

AC:

AN:

67214

Other (OTH)

AF:

0.000499

AC:

AN:

2006

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over