Genetic Variant MRPL9:c.589-15_589-5delTTTTTTTTTTT (chr1-151760903-CAAAAAAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_031420.4(MRPL9):c.589-15_589-5delTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000455 in 879,710 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: 0.0000045 ( 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]

MRPL9 links:

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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	Effect	Exon rank	MANE	Protein	UniProt
MRPL9	NM_031420.4 link	c.589-15_589-5delTTTTTTTTTTT	splice_region_variant, intron_variant	Intron 5 of 6	ENST00000368830.8	NP_113608.1	Q9BYD2
MRPL9	NM_001300733.2 link	c.487-15_487-5delTTTTTTTTTTT	splice_region_variant, intron_variant	Intron 4 of 5		NP_001287662.1	Q9BYD2Q5SZR1
MRPL9	NR_125331.2 link	n.646-15_646-5delTTTTTTTTTTT	splice_region_variant, intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL9	ENST00000368830.8 link	c.589-15_589-5delTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_031420.4	ENSP00000357823.3		Q9BYD2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000455

AC:

AN:

879710

Hom.:

AF XY:

0.00000458

AC XY:

AN XY:

437024

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

17788

American (AMR)

AF:

0.00

AC:

AN:

13256

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13542

East Asian (EAS)

AF:

0.00

AC:

AN:

29396

South Asian (SAS)

AF:

0.00

AC:

AN:

43464

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24420

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2684

European-Non Finnish (NFE)

AF:

0.00000574

AC:

AN:

697318

Other (OTH)

AF:

0.00

AC:

AN:

37842

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

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

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1-151760903-CAAAAAAAAAAAA-CA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over