Variant chr15-22865961-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_030922.7(NIPA2):c.449-252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,770 control chromosomes in the GnomAD database, including 16,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 16429 hom., cov: 31)

Consequence

NIPA2
NM_030922.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.295

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 15-22865961-C-T is Benign according to our data. Variant chr15-22865961-C-T is described in ClinVar as [Benign]. Clinvar id is 1280158.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIPA2	NM_030922.7 linkuse as main transcript	c.449-252C>T		intron_variant		ENST00000337451.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIPA2	ENST00000337451.8 linkuse as main transcript	c.449-252C>T		intron_variant		5	NM_030922.7	P1	Q8N8Q9-1

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65993

AN:

151652

Hom.:

16432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.555

Gnomad OTH

AF:

0.429

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.435

AC:

65987

AN:

151770

Hom.:

16429

Cov.:

AF XY:

0.438

AC XY:

32494

AN XY:

74146

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.655

Gnomad4 NFE

AF:

0.555

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.475

Hom.:

5944

Bravo

AF:

0.411

Asia WGS

AF:

0.352

AC:

1222

AN:

3478

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

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.87

DANN

Benign

0.60

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