5-177403624-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000505.4(F12):c.1251-7C>T 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 0.0000705 in 1,602,654 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_000505.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F12 | NM_000505.4 | c.1251-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000253496.4 | |||
F12 | XM_011534462.3 | c.915-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F12 | ENST00000253496.4 | c.1251-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000505.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000174 AC: 41AN: 235544Hom.: 0 AF XY: 0.000146 AC XY: 19AN XY: 129990
GnomAD4 exome AF: 0.0000441 AC: 64AN: 1450306Hom.: 0 Cov.: 31 AF XY: 0.0000388 AC XY: 28AN XY: 721570
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74490
ClinVar
Submissions by phenotype
Hereditary angioneurotic edema Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Factor XII deficiency disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Hereditary angioedema type 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Nephrolithiasis/osteoporosis, hypophosphatemic Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at