rs1134590
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000521393.1(IGHEP1):n.552G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 768,000 control chromosomes in the GnomAD database, including 198,530 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 0.74 ( 42417 hom., cov: 30)
Exomes 𝑓: 0.70 ( 156113 hom. )
Consequence
IGHEP1
ENST00000521393.1 non_coding_transcript_exon
ENST00000521393.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.196
Genes affected
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHEP1 | ENST00000521393.1 | n.552G>A | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.741 AC: 111825AN: 150944Hom.: 42380 Cov.: 30
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GnomAD3 exomes AF: 0.683 AC: 160797AN: 235534Hom.: 57834 AF XY: 0.693 AC XY: 88849AN XY: 128288
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GnomAD4 exome AF: 0.703 AC: 433826AN: 616940Hom.: 156113 Cov.: 0 AF XY: 0.708 AC XY: 237790AN XY: 336064
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GnomAD4 genome ? AF: 0.741 AC: 111897AN: 151060Hom.: 42417 Cov.: 30 AF XY: 0.728 AC XY: 53674AN XY: 73686
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at