rs11746980
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109865.1(MRPS30-DT):n.152+30866C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,012 control chromosomes in the GnomAD database, including 16,823 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 0.46 ( 16823 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
MRPS30-DT
NR_109865.1 intron, non_coding_transcript
NR_109865.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.911
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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS30-DT | NR_109865.1 | n.152+30866C>T | intron_variant, non_coding_transcript_variant | ||||
MRPS30-DT | NR_109862.1 | n.153-675C>T | intron_variant, non_coding_transcript_variant | ||||
MRPS30-DT | NR_109863.1 | n.153-675C>T | intron_variant, non_coding_transcript_variant | ||||
MRPS30-DT | NR_109864.1 | n.152+30866C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS30-DT | ENST00000503452.5 | n.136+30866C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.463 AC: 70330AN: 151892Hom.: 16781 Cov.: 33
GnomAD3 genomes
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70330
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151892
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33
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GnomAD4 genome ? AF: 0.463 AC: 70423AN: 152012Hom.: 16823 Cov.: 33 AF XY: 0.466 AC XY: 34610AN XY: 74296
GnomAD4 genome
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70423
AN:
152012
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33
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34610
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74296
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1949
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3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at