Variant 11-72225181-GGCTCCTTGCGGGCTGGCGTGGACCGGGA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001567.4(INPPL1):c.182+18_182+45del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,231,288 control chromosomes in the GnomAD database, including 10,303 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.087 ( 803 hom., cov: 30)

Exomes 𝑓: 0.13 ( 9500 hom. )

Consequence

INPPL1
NM_001567.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.222

Variant links:

Genes affected

INPPL1 (HGNC:6080): (inositol polyphosphate phosphatase like 1) The protein encoded by this gene is an SH2-containing 5'-inositol phosphatase that is involved in the regulation of insulin function. The encoded protein also plays a role in the regulation of epidermal growth factor receptor turnover and actin remodelling. Additionally, this gene supports metastatic growth in breast cancer and is a valuable biomarker for breast cancer. [provided by RefSeq, Jan 2009]

INPPL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-72225181-GGCTCCTTGCGGGCTGGCGTGGACCGGGA-G is Benign according to our data. Variant chr11-72225181-GGCTCCTTGCGGGCTGGCGTGGACCGGGA-G is described in ClinVar as [Benign]. Clinvar id is 1245110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72225181-GGCTCCTTGCGGGCTGGCGTGGACCGGGA-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INPPL1	NM_001567.4 linkuse as main transcript	c.182+18_182+45del		intron_variant		ENST00000298229.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPPL1	ENST00000298229.7 linkuse as main transcript	c.182+18_182+45del		intron_variant		1	NM_001567.4	P1	O15357-1
INPPL1	ENST00000541544.1 linkuse as main transcript	n.98+18_98+45del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0869

AC:

13211

AN:

152024

Hom.:

804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.0851

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0304

Gnomad FIN

AF:

0.0779

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.0435

AC:

113

AN:

2600

Hom.:

AF XY:

0.0517

AC XY:

AN XY:

1452

show subpopulations

Gnomad AFR exome

AF:

0.0119

Gnomad AMR exome

AF:

0.00667

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00595

Gnomad FIN exome

AF:

0.0185

Gnomad NFE exome

AF:

0.0682

Gnomad OTH exome

AF:

0.0217

GnomAD4 exome

AF:

0.129

AC:

138921

AN:

1079146

Hom.:

9500

AF XY:

0.129

AC XY:

65536

AN XY:

509686

show subpopulations

Gnomad4 AFR exome

AF:

0.0187

Gnomad4 AMR exome

AF:

0.0762

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.000224

Gnomad4 SAS exome

AF:

0.0314

Gnomad4 FIN exome

AF:

0.0881

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.0868

AC:

13208

AN:

152142

Hom.:

803

Cov.:

AF XY:

0.0829

AC XY:

6167

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0239

Gnomad4 AMR

AF:

0.0850

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.000582

Gnomad4 SAS

AF:

0.0303

Gnomad4 FIN

AF:

0.0779

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.0969

Hom.:

Bravo

AF:

0.0867

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 28, 2019	- -

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