GeneBe

rs755031728

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_031420.4(MRPL9):​c.589-14_589-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000587 in 953,902 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00042 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL9NM_031420.4 linkuse as main transcriptc.589-14_589-5del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000368830.8
MRPL9NM_001300733.2 linkuse as main transcriptc.487-14_487-5del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
MRPL9NR_125331.2 linkuse as main transcriptn.646-14_646-5del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL9ENST00000368830.8 linkuse as main transcriptc.589-14_589-5del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_031420.4 P1

Frequencies

GnomAD3 genomes
AF:
0.000404
AC:
30
AN:
74206
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00155
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000306
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000284
AC:
25
AN:
879702
Hom.:
0
AF XY:
0.0000252
AC XY:
11
AN XY:
437020
show subpopulations
Gnomad4 AFR exome
AF:
0.000955
Gnomad4 AMR exome
AF:
0.000226
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000460
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000793
GnomAD4 genome
AF:
0.000418
AC:
31
AN:
74200
Hom.:
0
Cov.:
0
AF XY:
0.000442
AC XY:
15
AN XY:
33964
show subpopulations
Gnomad4 AFR
AF:
0.00160
Gnomad4 AMR
AF:
0.000306
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs755031728; hg19: chr1-151733379; API