chr10-116592393-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006229.4(PNLIPRP1):c.205-23A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000528 in 1,571,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_006229.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNLIPRP1 | NM_006229.4 | c.205-23A>T | intron_variant | ENST00000358834.9 | |||
PNLIPRP1 | NM_001303135.1 | c.205-23A>T | intron_variant | ||||
PNLIPRP1 | XM_047425364.1 | c.205-23A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNLIPRP1 | ENST00000358834.9 | c.205-23A>T | intron_variant | 1 | NM_006229.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000265 AC: 6AN: 226742Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 121726
GnomAD4 exome AF: 0.0000528 AC: 75AN: 1419412Hom.: 0 Cov.: 36 AF XY: 0.0000443 AC XY: 31AN XY: 700426
GnomAD4 genome AF: 0.0000526 AC: 8AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74204
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at