Variant 15-22853374-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030922.7(NIPA2):c.196+123del variant causes a intron change. The variant allele was found at a frequency of 0.154 in 377,258 control chromosomes in the GnomAD database, including 197 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.050 ( 171 hom., cov: 23)

Exomes 𝑓: 0.21 ( 26 hom. )

Consequence

NIPA2
NM_030922.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.79

Variant links:

Genes affected

NIPA2 (HGNC:17044): (NIPA magnesium transporter 2) This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010]

NIPA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-22853374-CT-C is Benign according to our data. Variant chr15-22853374-CT-C is described in ClinVar as [Benign]. Clinvar id is 1245041.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIPA2	NM_030922.7 linkuse as main transcript	c.196+123del		intron_variant		ENST00000337451.8	NP_112184.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIPA2	ENST00000337451.8 linkuse as main transcript	c.196+123del		intron_variant		5	NM_030922.7	ENSP00000337618	P1	Q8N8Q9-1

Frequencies

GnomAD3 genomes

AF:

0.0499

AC:

6848

AN:

137100

Hom.:

172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0478

Gnomad AMI

AF:

0.00114

Gnomad AMR

AF:

0.0440

Gnomad ASJ

AF:

0.0832

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.0525

Gnomad FIN

AF:

0.0257

Gnomad MID

AF:

0.0925

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.0489

GnomAD4 exome

AF:

0.214

AC:

51391

AN:

240134

Hom.:

AF XY:

0.214

AC XY:

27784

AN XY:

129764

show subpopulations

Gnomad4 AFR exome

AF:

0.209

Gnomad4 AMR exome

AF:

0.182

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.297

Gnomad4 SAS exome

AF:

0.216

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.215

GnomAD4 genome

AF:

0.0500

AC:

6850

AN:

137124

Hom.:

171

Cov.:

AF XY:

0.0512

AC XY:

3374

AN XY:

65946

show subpopulations

Gnomad4 AFR

AF:

0.0479

Gnomad4 AMR

AF:

0.0440

Gnomad4 ASJ

AF:

0.0832

Gnomad4 EAS

AF:

0.218

Gnomad4 SAS

AF:

0.0520

Gnomad4 FIN

AF:

0.0257

Gnomad4 NFE

AF:

0.0416

Gnomad4 OTH

AF:

0.0512

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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