GeneBe

rs755031728

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_031420.4(MRPL9):​c.589-16_589-5delTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000114 in 879,720 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000011 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16

Publications

0 publications found
Variant links:
Genes affected
MRPL9 (HGNC:14277): (mitochondrial ribosomal protein L9) This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MRPL9NM_031420.4 linkc.589-16_589-5delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000368830.8 NP_113608.1 Q9BYD2
MRPL9NM_001300733.2 linkc.487-16_487-5delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 4 of 5 NP_001287662.1 Q9BYD2Q5SZR1
MRPL9NR_125331.2 linkn.646-16_646-5delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MRPL9ENST00000368830.8 linkc.589-16_589-5delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_031420.4 ENSP00000357823.3 Q9BYD2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000114
AC:
1
AN:
879720
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
437028
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
17792
American (AMR)
AF:
0.00
AC:
0
AN:
13256
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13542
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29398
South Asian (SAS)
AF:
0.00
AC:
0
AN:
43464
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24420
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2684
European-Non Finnish (NFE)
AF:
0.00000143
AC:
1
AN:
697322
Other (OTH)
AF:
0.00
AC:
0
AN:
37842
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs755031728; hg19: chr1-151733379; API