chr8-9007935-CTTTTTT-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_153332.4(ERI1):c.109-11_109-6del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 895,536 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000015 ( 0 hom., cov: 0)
Exomes 𝑓: 0.014 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
ERI1
NM_153332.4 intron
NM_153332.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.01
Genes affected
ERI1 (HGNC:23994): (exoribonuclease 1) Enables 3'-5' exonuclease activity. Predicted to be involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 8-9007935-CTTTTTT-C is Benign according to our data. Variant chr8-9007935-CTTTTTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 3037479.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.0138 (12355/895536) while in subpopulation EAS AF= 0.0181 (360/19930). AF 95% confidence interval is 0.0165. There are 1 homozygotes in gnomad4_exome. There are 6031 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERI1 | NM_153332.4 | c.109-11_109-6del | intron_variant | ENST00000250263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERI1 | ENST00000250263.8 | c.109-11_109-6del | intron_variant | 1 | NM_153332.4 | P1 | |||
ERI1 | ENST00000519292.5 | c.109-11_109-6del | intron_variant | 2 | P1 | ||||
ERI1 | ENST00000520684.5 | c.109-11_109-6del | intron_variant, NMD_transcript_variant | 5 | |||||
ERI1 | ENST00000521844.1 | c.*197-11_*197-6del | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 65322Hom.: 0 Cov.: 0 FAILED QC
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GnomAD4 exome AF: 0.0138 AC: 12355AN: 895536Hom.: 1 AF XY: 0.0135 AC XY: 6031AN XY: 448304
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000153 AC: 1AN: 65322Hom.: 0 Cov.: 0 AF XY: 0.0000345 AC XY: 1AN XY: 29010
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ERI1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 20, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at