15-22860320-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_030922.7(NIPA2):​c.288-309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,094 control chromosomes in the GnomAD database, including 16,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 16453 hom., cov: 33)

Consequence

NIPA2
NM_030922.7 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.85
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 Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 15-22860320-T-C is Benign according to our data. Variant chr15-22860320-T-C is described in ClinVar as [Benign]. Clinvar id is 1222352.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NIPA2NM_030922.7 linkuse as main transcriptc.288-309T>C intron_variant ENST00000337451.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NIPA2ENST00000337451.8 linkuse as main transcriptc.288-309T>C intron_variant 5 NM_030922.7 P1Q8N8Q9-1

Frequencies

GnomAD3 genomes
AF:
0.435
AC:
66129
AN:
151976
Hom.:
16456
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.190
Gnomad AMI
AF:
0.590
Gnomad AMR
AF:
0.439
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.280
Gnomad SAS
AF:
0.531
Gnomad FIN
AF:
0.654
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.555
Gnomad OTH
AF:
0.428
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.435
AC:
66122
AN:
152094
Hom.:
16453
Cov.:
33
AF XY:
0.438
AC XY:
32576
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.190
Gnomad4 AMR
AF:
0.439
Gnomad4 ASJ
AF:
0.393
Gnomad4 EAS
AF:
0.280
Gnomad4 SAS
AF:
0.530
Gnomad4 FIN
AF:
0.654
Gnomad4 NFE
AF:
0.555
Gnomad4 OTH
AF:
0.424
Alfa
AF:
0.473
Hom.:
2253
Bravo
AF:
0.412
Asia WGS
AF:
0.353
AC:
1228
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 submitterclinical testingGeneDxAug 20, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.8
DANN
Benign
0.67

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: rs12439822; hg19: chr15-23012748; API