rs55762796
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012188.5(FOXI1):c.*143A>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 0.0000489 in 694,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
FOXI1
NM_012188.5 3_prime_UTR
NM_012188.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.267
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXI1 | NM_012188.5 | c.*143A>G | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000306268.8 | NP_036320.2 | ||
FOXI1 | NM_144769.4 | c.*143A>G | 3_prime_UTR_variant | Exon 2 of 2 | NP_658982.1 | |||
FOXI1 | XR_941092.2 | n.1486A>G | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152142Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000184 AC: 10AN: 542436Hom.: 0 Cov.: 6 AF XY: 0.0000171 AC XY: 5AN XY: 292082
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GnomAD4 genome AF: 0.000158 AC: 24AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74428
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at