Genetic Variant INPP5B:c.*1210T>A (chr1-37930275-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000373021.1(INPP5B):c.*1210T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,044 control chromosomes in the GnomAD database, including 27,234 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 27234 hom., cov: 33)

Exomes 𝑓: 1.0 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

INPP5B
ENST00000373021.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130

Publications

9 publications found

Variant links:

Genes affected

INPP5B (HGNC:6077): (inositol polyphosphate-5-phosphatase B) This gene encodes a member of a family of inositol polyphosphate-5-phosphatases. These enzymes function in the regulation of calcium signaling by inactivating inositol phosphates. The encoded protein is localized to the cytosol and mitochondria, and associates with membranes through an isoprenyl modification near the C-terminus. Alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2014]

INPP5B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP5B	NM_005540.3 link	c.532+1638T>A		intron_variant	Intron 7 of 23	ENST00000373024.8	NP_005531.2	P32019-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
INPP5B	ENST00000373021.1 link	c.*1210T>A	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000362112.1	B1ARF3
INPP5B	ENST00000373024.8 link	c.532+1638T>A	intron_variant	Intron 7 of 23	1	NM_005540.3	ENSP00000362115.3	P32019-2
INPP5B	ENST00000373026.5 link	c.772+1398T>A	intron_variant	Intron 6 of 22	5		ENSP00000362117.1	P32019-1
INPP5B	ENST00000373027.5 link	c.40+1398T>A	intron_variant	Intron 1 of 17	2		ENSP00000362118.1	P32019-3

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86276

AN:

151924

Hom.:

27222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.449

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.523

Gnomad SAS

AF:

0.602

Gnomad FIN

AF:

0.744

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.586

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

Age Distribution

Exome Hom

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

GnomAD4 genome

AF:

0.568

AC:

86310

AN:

152044

Hom.:

27234

Cov.:

AF XY:

0.568

AC XY:

42204

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.272

AC:

11260

AN:

41470

American (AMR)

AF:

0.583

AC:

8903

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

2279

AN:

3472

East Asian (EAS)

AF:

0.523

AC:

2707

AN:

5176

South Asian (SAS)

AF:

0.604

AC:

2916

AN:

4828

European-Finnish (FIN)

AF:

0.744

AC:

7862

AN:

10574

Middle Eastern (MID)

AF:

0.582

AC:

171

AN:

294

European-Non Finnish (NFE)

AF:

0.715

AC:

48580

AN:

67952

Other (OTH)

AF:

0.581

AC:

1224

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1685

3370

5054

6739

8424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.630

Hom.:

4007

Bravo

AF:

0.537

Asia WGS

AF:

0.564

AC:

1961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

2.3

(source)

DANN

Benign

0.68

PhyloP100

-0.013

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over