20-35279894-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002212.4(EIF6):c.546+48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 1,597,916 control chromosomes in the GnomAD database, including 658,225 homozygotes. 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 0.94 ( 67317 hom., cov: 31)
Exomes 𝑓: 0.90 ( 590908 hom. )
Consequence
EIF6
NM_002212.4 intron
NM_002212.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0930
Genes affected
EIF6 (HGNC:6159): (eukaryotic translation initiation factor 6) Hemidesmosomes are structures which link the basal lamina to the intermediate filament cytoskeleton. An important functional component of hemidesmosomes is the integrin beta-4 subunit (ITGB4), a protein containing two fibronectin type III domains. The protein encoded by this gene binds to the fibronectin type III domains of ITGB4 and may help link ITGB4 to the intermediate filament cytoskeleton. The encoded protein, which is insoluble and found both in the nucleus and in the cytoplasm, can function as a translation initiation factor and prevent the association of the 40S and 60S ribosomal subunits. Multiple non-protein coding transcript variants and variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF6 | NM_002212.4 | c.546+48T>C | intron_variant | ENST00000374450.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF6 | ENST00000374450.8 | c.546+48T>C | intron_variant | 1 | NM_002212.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.939 AC: 142922AN: 152132Hom.: 67261 Cov.: 31
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GnomAD3 exomes AF: 0.940 AC: 228163AN: 242828Hom.: 107391 AF XY: 0.938 AC XY: 122786AN XY: 130938
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GnomAD4 exome AF: 0.903 AC: 1305828AN: 1445666Hom.: 590908 Cov.: 40 AF XY: 0.905 AC XY: 648901AN XY: 716828
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GnomAD4 genome ? AF: 0.939 AC: 143036AN: 152250Hom.: 67317 Cov.: 31 AF XY: 0.942 AC XY: 70161AN XY: 74448
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
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