chr7-128310672-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018077.3(RBM28):c.*125C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,304,646 control chromosomes in the GnomAD database, including 85,946 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 0.31 ( 8420 hom., cov: 31)
Exomes 𝑓: 0.36 ( 77526 hom. )
Consequence
RBM28
NM_018077.3 3_prime_UTR
NM_018077.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.625
Genes affected
RBM28 (HGNC:21863): (RNA binding motif protein 28) The protein encoded by this gene is a specific nucleolar component of the spliceosomal small nuclear ribonucleoprotein (snRNP)complexes . It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), possibly coordinating their transition through the nucleolus. Mutation in this gene causes alopecia, progressive neurological defects, and endocrinopathy (ANE syndrome), a pleiotropic and clinically heterogeneous disorder. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBM28 | NM_018077.3 | c.*125C>T | 3_prime_UTR_variant | 19/19 | ENST00000223073.6 | ||
RBM28 | NM_001166135.2 | c.*125C>T | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBM28 | ENST00000223073.6 | c.*125C>T | 3_prime_UTR_variant | 19/19 | 1 | NM_018077.3 | P1 | ||
RBM28 | ENST00000415472.6 | c.*125C>T | 3_prime_UTR_variant | 15/15 | 2 | ||||
RBM28 | ENST00000481788.1 | n.777C>T | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.309 AC: 46912AN: 151904Hom.: 8411 Cov.: 31
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GnomAD4 exome AF: 0.359 AC: 413448AN: 1152624Hom.: 77526 Cov.: 16 AF XY: 0.358 AC XY: 210301AN XY: 587752
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GnomAD4 genome AF: 0.309 AC: 46927AN: 152022Hom.: 8420 Cov.: 31 AF XY: 0.315 AC XY: 23372AN XY: 74306
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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