16-72060107-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS2
The NM_005143.5(HP):c.443-5G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000645 in 1,612,030 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_005143.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HP | NM_005143.5 | c.443-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000355906.10 | |||
HP | NM_001126102.3 | c.266-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
HP | NM_001318138.2 | c.266-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HP | ENST00000355906.10 | c.443-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005143.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000199 AC: 46AN: 231256Hom.: 2 AF XY: 0.000135 AC XY: 17AN XY: 125942
GnomAD4 exome AF: 0.0000610 AC: 89AN: 1459810Hom.: 1 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 726036
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74426
ClinVar
Submissions by phenotype
HP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 15, 2019 | This variant is classified as likely 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