rs7173238

Variant names:

• chr15-22853499-A-G
• rs7173238
• NM_030922.7:c.196+231A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-22853499-A-G
• chr15-22853499-A-C
• chr15-22853499-A-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_030922.7(NIPA2):​c.196+231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 151,286 control chromosomes in the GnomAD database, including 56,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.86 (56272 hom., cov: 26)
• Consequence: NIPA2 NM_030922.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.74
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BP6: Variant 15-22853499-A-G is Benign according to our data. Variant chr15-22853499-A-G is described in ClinVar as Benign. ClinVar VariationId is 1283116.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIPA2	NM_030922.7	MANE Select	c.196+231A>G		intron	N/A	NP_112184.4
	NIPA2	NM_001008860.3		c.196+231A>G		intron	N/A	NP_001008860.1	Q8N8Q9-1
	NIPA2	NM_001008892.3		c.196+231A>G		intron	N/A	NP_001008892.1	Q8N8Q9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIPA2	ENST00000337451.8	TSL:5 MANE Select	c.196+231A>G		intron	N/A	ENSP00000337618.3	Q8N8Q9-1
	NIPA2	ENST00000398013.7	TSL:1	c.196+231A>G		intron	N/A	ENSP00000381095.3	Q8N8Q9-1
	NIPA2	ENST00000359727.8	TSL:1	c.139+1629A>G		intron	N/A	ENSP00000352762.4	Q8N8Q9-2

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130259 AN: 151168 Hom.: 56225 Cov.: 26

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.862 AC: 130363 AN: 151286 Hom.: 56272 Cov.: 26 AF XY: 0.867 AC XY: 64028 AN XY: 73868

African (AFR) AF: 0.907 AC: 37385 AN: 41216

American (AMR) AF: 0.880 AC: 13365 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2694 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4729 AN: 5084

South Asian (SAS) AF: 0.909 AC: 4341 AN: 4774

European-Finnish (FIN) AF: 0.893 AC: 9330 AN: 10448

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55702 AN: 67814

Other (OTH) AF: 0.853 AC: 1791 AN: 2100

Alfa AF: 0.783 Hom.: 2350

Bravo AF: 0.863

Asia WGS AF: 0.899 AC: 3124 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.038
DANN	Benign	0.13
PhyloP100		-2.7

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

Other links and lift over

dbSNP: rs7173238; hg19: chr15-23019569;