chr1-30941990-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001020658.2(PUM1):c.3120+8A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000627 in 1,561,986 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001020658.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PUM1 | NM_001020658.2 | c.3120+8A>T | splice_region_variant, intron_variant | ENST00000426105.7 | |||
PUM1 | NM_014676.3 | c.3114+8A>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUM1 | ENST00000426105.7 | c.3120+8A>T | splice_region_variant, intron_variant | 1 | NM_001020658.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 472AN: 151762Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000827 AC: 208AN: 251394Hom.: 1 AF XY: 0.000559 AC XY: 76AN XY: 135874
GnomAD4 exome AF: 0.000355 AC: 501AN: 1410106Hom.: 1 Cov.: 30 AF XY: 0.000326 AC XY: 229AN XY: 702352
GnomAD4 genome AF: 0.00315 AC: 479AN: 151880Hom.: 1 Cov.: 30 AF XY: 0.00304 AC XY: 226AN XY: 74222
ClinVar
Submissions by phenotype
PUM1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at