Variant chr15-22860320-T-C 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.288-309T>C 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 152,094 control chromosomes in the GnomAD database, including 16,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 16453 hom., cov: 33)

Consequence

NIPA2
NM_030922.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.85

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=-0.85).

BP6

Variant 15-22860320-T-C is Benign according to our data. Variant chr15-22860320-T-C is described in ClinVar as [Benign]. Clinvar id is 1222352.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.288-309T>C		intron_variant		ENST00000337451.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIPA2	ENST00000337451.8 linkuse as main transcript	c.288-309T>C		intron_variant		5	NM_030922.7	P1	Q8N8Q9-1

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

66129

AN:

151976

Hom.:

16456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.531

Gnomad FIN

AF:

0.654

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.555

Gnomad OTH

AF:

0.428

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

GnomAD4 genome

AF:

0.435

AC:

66122

AN:

152094

Hom.:

16453

Cov.:

AF XY:

0.438

AC XY:

32576

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.190

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.654

Gnomad4 NFE

AF:

0.555

Gnomad4 OTH

AF:

0.424

Alfa

AF:

0.473

Hom.:

2253

Bravo

AF:

0.412

Asia WGS

AF:

0.353

AC:

1228

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

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.8

DANN

Benign

0.67

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