rs201403752

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_030922.7(NIPA2):​c.144A>C​(p.Gln48His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

NIPA2
NM_030922.7 missense

Scores

2
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.48
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29866186).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NIPA2NM_030922.7 linkc.144A>C p.Gln48His missense_variant Exon 5 of 8 ENST00000337451.8 NP_112184.4 Q8N8Q9-1A0A024R372

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NIPA2ENST00000337451.8 linkc.144A>C p.Gln48His missense_variant Exon 5 of 8 5 NM_030922.7 ENSP00000337618.3 Q8N8Q9-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
27
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.38
BayesDel_noAF
Benign
-0.20
CADD
Benign
22
DANN
Benign
0.92
DEOGEN2
Uncertain
0.46
T;T;T;.
LIST_S2
Benign
0.86
D;.;.;D
MetaRNN
Benign
0.30
T;T;T;T
PROVEAN
Benign
-1.3
N;N;N;N
Sift
Benign
0.17
T;T;T;T
Sift4G
Benign
0.20
T;T;T;T
Vest4
0.59
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
gMVP
0.82

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: rs201403752; hg19: chr15-23019852; API