rs8028189

chr15-22849067-C-Gchr15-22849067-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030922.7(NIPA2):c.-93-2572C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,008 control chromosomes in the GnomAD database, including 16,638 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (16638 hom., cov: 31)
• Consequence: NIPA2 NM_030922.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIPA2	NM_030922.7	c.-93-2572C>G		intron_variant		ENST00000337451.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIPA2	ENST00000337451.8	c.-93-2572C>G		intron_variant		5	NM_030922.7	P1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66439 AN: 151890 Hom.: 16641 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.437 AC: 66432 AN: 152008 Hom.: 16638 Cov.: 31 AF XY: 0.440 AC XY: 32728 AN XY: 74300

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.420

Alfa AF: 0.356 Hom.: 1072

Bravo AF: 0.413

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.37
Dann	Benign	0.28

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: rs8028189; hg19: chr15-23024001;