8-98193384-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_024759.3(NIPAL2):c.1067+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,612,268 control chromosomes in the GnomAD database, including 220,036 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_024759.3 splice_donor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIPAL2 | ENST00000430223.7 | c.1040-294G>A | intron_variant | Intron 10 of 10 | 1 | NM_001321635.2 | ENSP00000407087.2 | |||
NIPAL2 | ENST00000341166.3 | c.1067+1G>A | splice_donor_variant, intron_variant | Intron 11 of 11 | 2 | ENSP00000339256.3 | ||||
NIPAL2 | ENST00000520545.5 | n.1059-294G>A | intron_variant | Intron 9 of 9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.529 AC: 80415AN: 151894Hom.: 21398 Cov.: 32
GnomAD3 exomes AF: 0.542 AC: 136366AN: 251370Hom.: 37563 AF XY: 0.542 AC XY: 73653AN XY: 135836
GnomAD4 exome AF: 0.520 AC: 758742AN: 1460256Hom.: 198617 Cov.: 41 AF XY: 0.521 AC XY: 378176AN XY: 726472
GnomAD4 genome AF: 0.529 AC: 80485AN: 152012Hom.: 21419 Cov.: 32 AF XY: 0.533 AC XY: 39616AN XY: 74288
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at