5-170109167-A-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012188.5(FOXI1):c.*556A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 154,204 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 15 hom., cov: 32)
Exomes 𝑓: 0.0067 ( 0 hom. )
Consequence
FOXI1
NM_012188.5 3_prime_UTR
NM_012188.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.66
Genes affected
FOXI1 (HGNC:3815): (forkhead box I1) This gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. This gene may play an important role in the development of the cochlea and vestibulum, as well as in embryogenesis. The encoded protein has been found to be required for the transcription of four subunits of a proton pump found in the inner ear, the kidney, and the epididymis. Mutations in this gene have been associated with deafness, autosomal recessive 4. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 5-170109167-A-G is Benign according to our data. Variant chr5-170109167-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 905481.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXI1 | NM_012188.5 | c.*556A>G | 3_prime_UTR_variant | 2/2 | ENST00000306268.8 | ||
FOXI1 | NM_144769.4 | c.*556A>G | 3_prime_UTR_variant | 2/2 | |||
FOXI1 | XR_941092.2 | n.1899A>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXI1 | ENST00000306268.8 | c.*556A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_012188.5 | P1 | ||
FOXI1 | ENST00000449804.4 | c.*556A>G | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0108 AC: 1648AN: 152152Hom.: 15 Cov.: 32
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GnomAD4 exome AF: 0.00672 AC: 13AN: 1934Hom.: 0 Cov.: 0 AF XY: 0.00818 AC XY: 8AN XY: 978
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GnomAD4 genome AF: 0.0108 AC: 1647AN: 152270Hom.: 15 Cov.: 32 AF XY: 0.0115 AC XY: 856AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 05, 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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at