15-22858387-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_030922.7(NIPA2):c.197-153C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,030 control chromosomes in the GnomAD database, including 315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.054 (315 hom., cov: 33)
• Consequence: NIPA2 NM_030922.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.181

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 15-22858387-C-G is Benign according to our data. Variant chr15-22858387-C-G is described in ClinVar as [Benign]. Clinvar id is 1264605.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIPA2	NM_030922.7	c.197-153C>G		intron_variant		ENST00000337451.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIPA2	ENST00000337451.8	c.197-153C>G		intron_variant		5	NM_030922.7	P1

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8234 AN: 151912 Hom.: 316 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0542 AC: 8239 AN: 152030 Hom.: 315 Cov.: 33 AF XY: 0.0551 AC XY: 4093 AN XY: 74300

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0872

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.0489

Alfa AF: 0.0598 Hom.: 55

Bravo AF: 0.0540

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs138141434; hg19: chr15-23014681;