GeneBe

rs35568106

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_030922.7(NIPA2):​c.196+117_196+123delTTTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000823 in 242,930 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000082 ( 0 hom. )

Consequence

NIPA2
NM_030922.7 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.79

Publications

0 publications found
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030922.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NIPA2
NM_030922.7
MANE Select
c.196+117_196+123delTTTTTTT
intron
N/ANP_112184.4
NIPA2
NM_001008860.3
c.196+117_196+123delTTTTTTT
intron
N/ANP_001008860.1Q8N8Q9-1
NIPA2
NM_001008892.3
c.196+117_196+123delTTTTTTT
intron
N/ANP_001008892.1Q8N8Q9-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NIPA2
ENST00000337451.8
TSL:5 MANE Select
c.196+107_196+113delTTTTTTT
intron
N/AENSP00000337618.3Q8N8Q9-1
NIPA2
ENST00000398013.7
TSL:1
c.196+107_196+113delTTTTTTT
intron
N/AENSP00000381095.3Q8N8Q9-1
NIPA2
ENST00000359727.8
TSL:1
c.139+1505_139+1511delTTTTTTT
intron
N/AENSP00000352762.4Q8N8Q9-2

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
0.00000823
AC:
2
AN:
242930
Hom.:
0
AF XY:
0.00000762
AC XY:
1
AN XY:
131314
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
6040
American (AMR)
AF:
0.000108
AC:
1
AN:
9276
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
6552
East Asian (EAS)
AF:
0.00
AC:
0
AN:
15454
South Asian (SAS)
AF:
0.00
AC:
0
AN:
22258
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
14414
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1186
European-Non Finnish (NFE)
AF:
0.00000645
AC:
1
AN:
155082
Other (OTH)
AF:
0.00
AC:
0
AN:
12668
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs35568106; hg19: chr15-23019694; API