Variant 15-22853498-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.196+230C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 151,242 control chromosomes in the GnomAD database, including 741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.073 ( 741 hom., cov: 28)

Consequence

NIPA2
NM_030922.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.10

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=-1.02).

BP6

Variant 15-22853498-C-T is Benign according to our data. Variant chr15-22853498-C-T is described in ClinVar as [Benign]. Clinvar id is 1220955.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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+230C>T		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+230C>T		intron_variant		5	NM_030922.7	ENSP00000337618	P1	Q8N8Q9-1

Frequencies

GnomAD3 genomes

AF:

0.0725

AC:

10951

AN:

151124

Hom.:

738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.0435

Gnomad ASJ

AF:

0.0859

Gnomad EAS

AF:

0.000390

Gnomad SAS

AF:

0.0224

Gnomad FIN

AF:

0.0423

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0273

Gnomad OTH

AF:

0.0713

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

GnomAD4 genome

AF:

0.0726

AC:

10973

AN:

151242

Hom.:

741

Cov.:

AF XY:

0.0725

AC XY:

5353

AN XY:

73880

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.0434

Gnomad4 ASJ

AF:

0.0859

Gnomad4 EAS

AF:

0.000391

Gnomad4 SAS

AF:

0.0226

Gnomad4 FIN

AF:

0.0423

Gnomad4 NFE

AF:

0.0273

Gnomad4 OTH

AF:

0.0705

Alfa

AF:

0.0630

Hom.:

Bravo

AF:

0.0778

Asia WGS

AF:

0.0200

AC:

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

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.36

DANN

Benign

0.49

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