rs531550505
Positions:
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-A
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
- chr15-22786677-AGCGGCGGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_144599.5(NIPA1):c.27_47del(p.Ala10_Ala16del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000448 in 1,071,500 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A8A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000034 ( 0 hom., cov: 6)
Exomes 𝑓: 0.000046 ( 3 hom. )
Consequence
NIPA1
NM_144599.5 inframe_deletion
NM_144599.5 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.48
Genes affected
NIPA1 (HGNC:17043): (NIPA magnesium transporter 1) This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. This protein may play a role in nervous system development and maintenance. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with autosomal dominant spastic paraplegia 6. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_144599.5
BS2
?
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| NIPA1 | NM_144599.5 | c.27_47del | p.Ala10_Ala16del | inframe_deletion | 1/5 | ENST00000337435.9 | |
| NIPA1 | NM_001142275.1 | c.-48+435_-48+455del | intron_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NIPA1 | ENST00000337435.9 | c.27_47del | p.Ala10_Ala16del | inframe_deletion | 1/5 | 1 | NM_144599.5 | P1 | |
| NIPA1 | ENST00000437912.6 | c.-48+12370_-48+12390del | intron_variant | 1 | |||||
| NIPA1 | ENST00000561183.5 | c.-48+435_-48+455del | intron_variant | 1 | |||||
| NIPA1 | ENST00000560069.5 | n.31+435_31+455del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000344 AC: 5AN: 145406Hom.: 0 Cov.: 6
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GnomAD3 exomes AF: 0.000347 AC: 7AN: 20176Hom.: 1 AF XY: 0.000474 AC XY: 6AN XY: 12652
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GnomAD4 exome AF: 0.0000464 AC: 43AN: 926094Hom.: 3 AF XY: 0.0000723 AC XY: 32AN XY: 442826
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GnomAD4 genome ? AF: 0.0000344 AC: 5AN: 145406Hom.: 0 Cov.: 6 AF XY: 0.0000424 AC XY: 3AN XY: 70686
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at