15-22786677-AGCGGCGGCGGCGGCGGCG-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_144599.5(NIPA1):c.30_47del(p.Ala11_Ala16del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000308 in 1,071,498 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_144599.5 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPA1 | NM_144599.5 | c.30_47del | p.Ala11_Ala16del | inframe_deletion | 1/5 | ENST00000337435.9 | |
NIPA1 | NM_001142275.1 | c.-48+438_-48+455del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPA1 | ENST00000337435.9 | c.30_47del | p.Ala11_Ala16del | inframe_deletion | 1/5 | 1 | NM_144599.5 | P1 | |
NIPA1 | ENST00000437912.6 | c.-48+12373_-48+12390del | intron_variant | 1 | |||||
NIPA1 | ENST00000561183.5 | c.-48+438_-48+455del | intron_variant | 1 | |||||
NIPA1 | ENST00000560069.5 | n.31+438_31+455del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000688 AC: 1AN: 145406Hom.: 0 Cov.: 6
GnomAD4 exome AF: 0.0000346 AC: 32AN: 926092Hom.: 0 AF XY: 0.0000406 AC XY: 18AN XY: 442826
GnomAD4 genome AF: 0.00000688 AC: 1AN: 145406Hom.: 0 Cov.: 6 AF XY: 0.0000141 AC XY: 1AN XY: 70686
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at