chr15-22851841-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030922.7(NIPA2):c.110G>A(p.Arg37Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,613,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
NIPA2
NM_030922.7 missense
NM_030922.7 missense
Scores
1
3
5
Clinical Significance
Conservation
PhyloP100: 6.79
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 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=0.37010342).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPA2 | NM_030922.7 | c.110G>A | p.Arg37Gln | missense_variant | 4/8 | ENST00000337451.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPA2 | ENST00000337451.8 | c.110G>A | p.Arg37Gln | missense_variant | 4/8 | 5 | NM_030922.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251218Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135778
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GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461434Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727040
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74444
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2022 | The c.110G>A (p.R37Q) alteration is located in exon 6 (coding exon 1) of the NIPA2 gene. This alteration results from a G to A substitution at nucleotide position 110, causing the arginine (R) at amino acid position 37 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.;D;D;.;.
LIST_S2
Uncertain
D;D;.;.;D;.
MetaRNN
Benign
T;T;T;T;T;T
PROVEAN
Benign
N;N;N;N;N;N
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Vest4
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at