Genetic Variant NM_005540.3:c.152C>A (chr1-37945756-G-T) – ACMG Classification: Uncertain_significance (4 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM5

The NM_005540.3(INPP5B):c.152C>A(p.Ala51Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000685 in 1,460,328 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A51V) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

INPP5B
NM_005540.3 missense, splice_region

Scores

Splicing: ADA: 0.9488

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.92

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:

LOC105378651 (HGNC:):

LOC105378651 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr1-37945756-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 548655.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPP5B	NM_005540.3 link	c.152C>A	p.Ala51Asp	missense_variant, splice_region_variant	Exon 3 of 24	ENST00000373024.8	NP_005531.2	P32019-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
INPP5B	ENST00000373024.8 link	c.152C>A	p.Ala51Asp	missense_variant, splice_region_variant	Exon 3 of 24	1	NM_005540.3	ENSP00000362115.3	P32019-2
INPP5B	ENST00000373026.5 link	c.152C>A	p.Ala51Asp	missense_variant, splice_region_variant	Exon 2 of 23	5		ENSP00000362117.1	P32019-1
INPP5B	ENST00000373021.1 link	c.152C>A	p.Ala51Asp	missense_variant, splice_region_variant	Exon 2 of 6	1		ENSP00000362112.1	B1ARF3
INPP5B	ENST00000491406.2 link	n.240C>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 7	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.85e-7

AC:

AN:

1460328

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726538

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:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.00e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.86

BayesDel_addAF

Pathogenic

0.30

BayesDel_noAF

Pathogenic

0.19

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.10

T;T;T;.;.

Eigen

Uncertain

0.59

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.78

T;.;T;T;T

M_CAP

Uncertain

0.12

MetaRNN

Uncertain

0.59

D;D;D;D;D

MetaSVM

Pathogenic

0.81

PrimateAI

Uncertain

0.65

PROVEAN

Benign

-1.6

.;N;N;N;D

REVEL

Uncertain

0.61

Sift

Pathogenic

0.0

.;D;D;D;D

Sift4G

Benign

0.073

T;D;D;T;D

Polyphen

1.0

.;.;.;D;.

Vest4

0.82

MutPred

0.41

Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);

MVP

0.97

MPC

0.97

ClinPred

1.0

GERP RS

4.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.65

gMVP

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.95

dbscSNV1_RF

Pathogenic

0.83

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over