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15-22858577-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

The NM_030922.7(NIPA2):c.234G>A(p.Ala78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,604,088 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00093 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 1 hom. )

Consequence

NIPA2
NM_030922.7 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.21
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 15-22858577-G-A is Benign according to our data. Variant chr15-22858577-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3051412.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.21 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NIPA2NM_030922.7 linkuse as main transcriptc.234G>A p.Ala78= synonymous_variant 6/8 ENST00000337451.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NIPA2ENST00000337451.8 linkuse as main transcriptc.234G>A p.Ala78= synonymous_variant 6/85 NM_030922.7 P1Q8N8Q9-1

Frequencies

GnomAD3 genomes
AF:
0.000927
AC:
141
AN:
152124
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00328
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000261
AC:
62
AN:
237566
Hom.:
1
AF XY:
0.000218
AC XY:
28
AN XY:
128214
show subpopulations
Gnomad AFR exome
AF:
0.00321
Gnomad AMR exome
AF:
0.000181
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000138
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000375
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000107
AC:
156
AN:
1451846
Hom.:
1
Cov.:
29
AF XY:
0.0000943
AC XY:
68
AN XY:
721250
show subpopulations
Gnomad4 AFR exome
AF:
0.00306
Gnomad4 AMR exome
AF:
0.000390
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000102
Gnomad4 SAS exome
AF:
0.0000590
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000542
Gnomad4 OTH exome
AF:
0.000367
GnomAD4 genome
AF:
0.000926
AC:
141
AN:
152242
Hom.:
1
Cov.:
33
AF XY:
0.000981
AC XY:
73
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.00327
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.0000226
Hom.:
0
Bravo
AF:
0.00106

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

NIPA2-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesMar 01, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.32
Cadd
Benign
2.6
Dann
Benign
0.62
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs146520013; hg19: chr15-23014491; API