chr1-209786025-C-CT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_006147.4(IRF6):c.*2394_*2395insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0091 in 152,230 control chromosomes in the GnomAD database, including 28 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0091 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IRF6
NM_006147.4 3_prime_UTR
NM_006147.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.322
Genes affected
IRF6 (HGNC:6121): (interferon regulatory factor 6) This gene encodes a member of the interferon regulatory transcription factor (IRF) family. Family members share a highly-conserved N-terminal helix-turn-helix DNA-binding domain and a less conserved C-terminal protein-binding domain. The encoded protein may be a transcriptional activator. Mutations in this gene can cause van der Woude syndrome and popliteal pterygium syndrome. Mutations in this gene are also associated with non-syndromic orofacial cleft type 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-209786025-C-CT is Benign according to our data. Variant chr1-209786025-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 295172.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0091 (1385/152230) while in subpopulation AFR AF= 0.0317 (1317/41542). AF 95% confidence interval is 0.0303. There are 28 homozygotes in gnomad4. There are 629 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1381 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF6 | NM_006147.4 | c.*2394_*2395insA | 3_prime_UTR_variant | 9/9 | ENST00000367021.8 | ||
IRF6 | NM_001206696.2 | c.*2394_*2395insA | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF6 | ENST00000367021.8 | c.*2394_*2395insA | 3_prime_UTR_variant | 9/9 | 1 | NM_006147.4 | P1 | ||
IRF6 | ENST00000542854.5 | c.*2394_*2395insA | 3_prime_UTR_variant | 7/7 | 2 | ||||
IRF6 | ENST00000696134.1 | c.*3225_*3226insA | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 |
Frequencies
GnomAD3 genomes ? AF: 0.00908 AC: 1381AN: 152112Hom.: 27 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 12Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 10
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Data not reliable, filtered out with message: AC0;AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Popliteal pterygium syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Cleft Lip +/- Cleft Palate, Autosomal Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Van der Woude syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at