chr1-209796557-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006147.4(IRF6):c.175-5C>G 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 0.346 in 1,609,454 control chromosomes in the GnomAD database, including 98,133 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_006147.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF6 | NM_006147.4 | c.175-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000367021.8 | |||
IRF6 | NM_001206696.2 | c.-111-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF6 | ENST00000367021.8 | c.175-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006147.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.320 AC: 48465AN: 151492Hom.: 7901 Cov.: 31
GnomAD3 exomes AF: 0.322 AC: 80731AN: 250510Hom.: 13527 AF XY: 0.324 AC XY: 43846AN XY: 135430
GnomAD4 exome AF: 0.349 AC: 508331AN: 1457842Hom.: 90233 Cov.: 35 AF XY: 0.348 AC XY: 252696AN XY: 725332
GnomAD4 genome AF: 0.320 AC: 48477AN: 151612Hom.: 7900 Cov.: 31 AF XY: 0.317 AC XY: 23510AN XY: 74092
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal dominant popliteal pterygium syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Van der Woude syndrome;C0265259:Popliteal pterygium syndrome;C1837213:Orofacial cleft 6, susceptibility to Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Van der Woude syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at