chr15-22853374-CTTTTT-C

Variant names:

• chr15-22853374-CTTTTT-C
• rs35568106
• NM_030922.7:c.196+119_196+123delTTTTT

Variant summary

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

The NM_030922.7(NIPA2):​c.196+119_196+123delTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.000841 in 242,600 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: 𝑓 0.0 (0 hom., cov: 23)
  • Exomes 𝑓: 0.00084 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NIPA2 NM_030922.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.79
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIPA2	NM_030922.7	c.196+119_196+123delTTTTT		intron_variant	Intron 5 of 7	ENST00000337451.8	NP_112184.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIPA2	ENST00000337451.8	c.196+107_196+111delTTTTT		intron_variant	Intron 5 of 7	5	NM_030922.7	ENSP00000337618.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 137238 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000841 AC: 204 AN: 242600 Hom.: 0 AF XY: 0.000908 AC XY: 119 AN XY: 131124

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000829 AC: 5 AN: 6034

American (AMR) AF: 0.00227 AC: 21 AN: 9250

Ashkenazi Jewish (ASJ) AF: 0.00122 AC: 8 AN: 6536

East Asian (EAS) AF: 0.000777 AC: 12 AN: 15438

South Asian (SAS) AF: 0.000991 AC: 22 AN: 22208

European-Finnish (FIN) AF: 0.000694 AC: 10 AN: 14404

Middle Eastern (MID) AF: 0.000843 AC: 1 AN: 1186

European-Non Finnish (NFE) AF: 0.000749 AC: 116 AN: 154896

Other (OTH) AF: 0.000712 AC: 9 AN: 12648

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 137238 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 65962

African (AFR) AF: 0.00 AC: 0 AN: 37140

American (AMR) AF: 0.00 AC: 0 AN: 13432

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3284

East Asian (EAS) AF: 0.00 AC: 0 AN: 4702

South Asian (SAS) AF: 0.00 AC: 0 AN: 4368

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7722

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63558

Other (OTH) AF: 0.00 AC: 0 AN: 1866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs35568106; hg19: chr15-23019694;