Genetic Variant MRPL9:c.589-9_589-5delTTTTT (chr1-151760903-CAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The ENST00000368830.8(MRPL9):c.589-9_589-5delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000894 in 951,064 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 0.000067 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00096 ( 0 hom. )

Consequence

MRPL9
ENST00000368830.8 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.93

Publications

1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368830.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MRPL9	NM_031420.4	MANE Select	c.589-9_589-5delTTTTT	splice_region intron	N/A	NP_113608.1
MRPL9	NM_001300733.2		c.487-9_487-5delTTTTT	splice_region intron	N/A	NP_001287662.1
MRPL9	NR_125331.2		n.646-9_646-5delTTTTT	splice_region intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MRPL9	ENST00000368830.8	TSL:1 MANE Select	c.589-9_589-5delTTTTT	splice_region intron	N/A	ENSP00000357823.3
MRPL9	ENST00000495867.1	TSL:2	n.13_17delTTTTT	non_coding_transcript_exon	Exon 1 of 2
MRPL9	ENST00000368829.3	TSL:2	c.487-9_487-5delTTTTT	splice_region intron	N/A	ENSP00000357822.3

Frequencies

GnomAD3 genomes

AF:

0.0000674

AC:

AN:

74204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000377

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00893

Gnomad NFE

AF:

0.0000768

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000964

AC:

845

AN:

876866

Hom.:

AF XY:

0.000976

AC XY:

425

AN XY:

435562

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000788

AC:

AN:

17756

American (AMR)

AF:

0.000987

AC:

AN:

13174

Ashkenazi Jewish (ASJ)

AF:

0.00111

AC:

AN:

13502

East Asian (EAS)

AF:

0.000785

AC:

AN:

29292

South Asian (SAS)

AF:

0.00162

AC:

AN:

43194

European-Finnish (FIN)

AF:

0.000492

AC:

AN:

24370

Middle Eastern (MID)

AF:

0.000747

AC:

AN:

2678

European-Non Finnish (NFE)

AF:

0.000964

AC:

670

AN:

695164

Other (OTH)

AF:

0.000689

AC:

AN:

37736

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.258

Heterozygous variant carriers

103

207

310

414

517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

104

130

<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

AF:

0.0000674

AC:

AN:

74198

Hom.:

Cov.:

AF XY:

0.0000589

AC XY:

AN XY:

33964

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18078

American (AMR)

AF:

0.00

AC:

AN:

6544

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2212

East Asian (EAS)

AF:

0.000379

AC:

AN:

2640

South Asian (SAS)

AF:

0.00

AC:

AN:

2044

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2006

Middle Eastern (MID)

AF:

0.00980

AC:

AN:

102

European-Non Finnish (NFE)

AF:

0.0000769

AC:

AN:

39032

Other (OTH)

AF:

0.00

AC:

AN:

994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.9

Mutation Taster

=93/7

polymorphism

(source)

Splicing

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

Publications

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1-151760903-CAAAAAAAAAAAA-CAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over