rs248247
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000518219.5(MRNIP):c.*47C>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 0.349 in 999,016 control chromosomes in the GnomAD database, including 63,339 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 0.32 ( 8241 hom., cov: 33)
Exomes 𝑓: 0.35 ( 55098 hom. )
Consequence
MRNIP
ENST00000518219.5 3_prime_UTR
ENST00000518219.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.38
Genes affected
MRNIP (HGNC:30817): (MRN complex interacting protein) Enables chromatin binding activity. Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; regulation of double-strand break repair; and response to ionizing radiation. Located in nucleoplasm. Colocalizes with Mre11 complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRNIP | NM_016175.4 | c.537+89C>T | intron_variant | ENST00000292586.11 | |||
MRNIP | NM_001017987.3 | c.372+89C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRNIP | ENST00000292586.11 | c.537+89C>T | intron_variant | 1 | NM_016175.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.317 AC: 48011AN: 151676Hom.: 8235 Cov.: 33
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GnomAD3 exomes AF: 0.354 AC: 52209AN: 147398Hom.: 9819 AF XY: 0.360 AC XY: 28118AN XY: 78090
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GnomAD4 exome AF: 0.355 AC: 300749AN: 847222Hom.: 55098 Cov.: 11 AF XY: 0.358 AC XY: 155884AN XY: 435756
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GnomAD4 genome ? AF: 0.316 AC: 48030AN: 151794Hom.: 8241 Cov.: 33 AF XY: 0.325 AC XY: 24076AN XY: 74178
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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