Genetic Variant NM_001567.4:c.987A>G (chr11-72230168-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001567.4(INPPL1):c.987A>G(p.Ser329Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,610,878 control chromosomes in the GnomAD database, including 39,762 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7134 hom., cov: 33)

Exomes 𝑓: 0.20 ( 32628 hom. )

Consequence

INPPL1
NM_001567.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.77

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-72230168-A-G is Benign according to our data. Variant chr11-72230168-A-G is described in ClinVar as [Benign]. Clinvar id is 1170422.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72230168-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.77 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INPPL1	NM_001567.4 link	c.987A>G	p.Ser329Ser	synonymous_variant	Exon 9 of 28	ENST00000298229.7	NP_001558.3	O15357-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
INPPL1	ENST00000298229.7 link	c.987A>G	p.Ser329Ser	synonymous_variant	Exon 9 of 28	1	NM_001567.4	ENSP00000298229.2	O15357-1
INPPL1	ENST00000538751.5 link	c.261A>G	p.Ser87Ser	synonymous_variant	Exon 8 of 27	1		ENSP00000444619.1	O15357-2
INPPL1	ENST00000540329.5 link	c.171A>G	p.Ser57Ser	synonymous_variant	Exon 6 of 7	3		ENSP00000440018.1	F5GY16

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41943

AN:

152140

Hom.:

7131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.234

GnomAD3 exomes

AF:

0.243

AC:

60662

AN:

249322

Hom.:

8573

AF XY:

0.242

AC XY:

32583

AN XY:

134660

show subpopulations

Gnomad AFR exome

AF:

0.487

Gnomad AMR exome

AF:

0.254

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.324

Gnomad SAS exome

AF:

0.359

Gnomad FIN exome

AF:

0.210

Gnomad NFE exome

AF:

0.175

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.199

AC:

290834

AN:

1458620

Hom.:

32628

Cov.:

AF XY:

0.203

AC XY:

146981

AN XY:

725010

show subpopulations

Gnomad4 AFR exome

AF:

0.494

Gnomad4 AMR exome

AF:

0.249

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.285

Gnomad4 SAS exome

AF:

0.348

Gnomad4 FIN exome

AF:

0.206

Gnomad4 NFE exome

AF:

0.173

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.276

AC:

41980

AN:

152258

Hom.:

7134

Cov.:

AF XY:

0.279

AC XY:

20771

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.477

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.337

Gnomad4 SAS

AF:

0.357

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.197

Hom.:

5400

Bravo

AF:

0.285

Asia WGS

AF:

0.379

AC:

1318

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Aug 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Opsismodysplasia

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.53

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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