rs2305491
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003310.5(EIPR1):c.654-238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 367,636 control chromosomes in the GnomAD database, including 138,235 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 0.86 ( 56580 hom., cov: 30)
Exomes 𝑓: 0.86 ( 81655 hom. )
Consequence
EIPR1
NM_003310.5 intron
NM_003310.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.446
Genes affected
EIPR1 (HGNC:12383): (EARP complex and GARP complex interacting protein 1) This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene resides on chromosome 2 rather than chromosome 11. [provided by RefSeq, Dec 2008]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIPR1 | NM_003310.5 | c.654-238G>A | intron_variant | ENST00000382125.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIPR1 | ENST00000382125.9 | c.654-238G>A | intron_variant | 1 | NM_003310.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.859 AC: 130454AN: 151932Hom.: 56544 Cov.: 30
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GnomAD4 exome AF: 0.863 AC: 186028AN: 215586Hom.: 81655 Cov.: 4 AF XY: 0.863 AC XY: 94931AN XY: 109948
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GnomAD4 genome ? AF: 0.859 AC: 130551AN: 152050Hom.: 56580 Cov.: 30 AF XY: 0.854 AC XY: 63493AN XY: 74320
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ClinVar
Not reported inComputational scores
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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