Genetic Variant NM_001272013.2:c.-13-10399G>A (chr10-104326463-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001272013.2(ITPRIP):c.-13-10399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,288 control chromosomes in the GnomAD database, including 1,796 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 0.10 ( 1796 hom., cov: 32)

Exomes 𝑓: 0.057 ( 0 hom. )

Consequence

ITPRIP
NM_001272013.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Publications

0 publications found

Variant links:

Genes affected

ITPRIP (HGNC:29370): (inositol 1,4,5-trisphosphate receptor interacting protein) This gene encodes a membrane-associated protein that binds the inositol 1,4,5-trisphosphate receptor (ITPR). The encoded protein enhances the sensitivity of ITPR to intracellular calcium signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

ITPRIP links:

ITPRIP-AS1 (HGNC:54100): (ITPRIP antisense RNA 1)

ITPRIP-AS1 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001272013.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITPRIP	NM_001272013.2	MANE Select	c.-13-10399G>A	intron	N/A	NP_001258942.1	Q8IWB1
ITPRIP	NM_001272012.2		c.-14+2402G>A	intron	N/A	NP_001258941.1	Q8IWB1
ITPRIP	NM_033397.4		c.-14+6875G>A	intron	N/A	NP_203755.1	Q8IWB1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITPRIP	ENST00000337478.3	TSL:1 MANE Select	c.-13-10399G>A	intron	N/A	ENSP00000337178.1	Q8IWB1
ITPRIP	ENST00000278071.6	TSL:1	c.-14+6875G>A	intron	N/A	ENSP00000278071.2	Q8IWB1
ITPRIP	ENST00000458723.1	TSL:1	c.-14+6875G>A	intron	N/A	ENSP00000414141.1	X6RK76

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15905

AN:

152100

Hom.:

1786

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0509

Gnomad ASJ

AF:

0.0994

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.0308

Gnomad FIN

AF:

0.0398

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0238

Gnomad OTH

AF:

0.0781

GnomAD4 exome

AF:

0.0571

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0714

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0625

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.105

AC:

15937

AN:

152218

Hom.:

1796

Cov.:

AF XY:

0.104

AC XY:

7735

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.285

AC:

11825

AN:

41498

American (AMR)

AF:

0.0508

AC:

778

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0994

AC:

345

AN:

3470

East Asian (EAS)

AF:

0.120

AC:

618

AN:

5166

South Asian (SAS)

AF:

0.0313

AC:

151

AN:

4826

European-Finnish (FIN)

AF:

0.0398

AC:

422

AN:

10610

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0238

AC:

1617

AN:

68030

Other (OTH)

AF:

0.0791

AC:

167

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

630

1261

1891

2522

3152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0800

Hom.:

173

Bravo

AF:

0.115

Asia WGS

AF:

0.101

AC:

352

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.90

(source)

DANN

Benign

0.91

PhyloP100

-1.7

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over