Genetic Variant MRPL9:c.589-5_589-4insTTTTTTTTTTTTTTTTTTTTTTTTT (chr1-151760903-C-CAAAAAAAAAAAAAAAAAAAAAAAAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_031420.4(MRPL9):c.589-5_589-4insTTTTTTTTTTTTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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: 𝑓 0.00016 ( 3 hom., cov: 0)

Exomes 𝑓: 0.000042 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.153

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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031420.4. 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.589-5_589-4insTTTTTTTTTTTTTTTTTTTTTTTTT	splice_region intron	N/A	NP_113608.1
MRPL9	NM_001300733.2		c.487-5_487-4insTTTTTTTTTTTTTTTTTTTTTTTTT	splice_region intron	N/A	NP_001287662.1
MRPL9	NR_125331.2		n.646-5_646-4insTTTTTTTTTTTTTTTTTTTTTTTTT	splice_region intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MRPL9	ENST00000368830.8	TSL:1 MANE Select	c.589-5_589-4insTTTTTTTTTTTTTTTTTTTTTTTTT	splice_region intron	N/A	ENSP00000357823.3
MRPL9	ENST00000495867.1	TSL:2	n.17_18insTTTTTTTTTTTTTTTTTTTTTTTTT	non_coding_transcript_exon	Exon 1 of 2
MRPL9	ENST00000368829.3	TSL:2	c.487-5_487-4insTTTTTTTTTTTTTTTTTTTTTTTTT	splice_region intron	N/A	ENSP00000357822.3

Frequencies

GnomAD3 genomes

AF:

0.000162

AC:

AN:

74204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000332

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000153

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:

0.000128

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000421

AC:

AN:

879698

Hom.:

Cov.:

AF XY:

0.0000481

AC XY:

AN XY:

437016

show subpopulations

African (AFR)

AF:

0.000225

AC:

AN:

17790

American (AMR)

AF:

0.0000754

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:

0.000184

AC:

AN:

43464

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2684

European-Non Finnish (NFE)

AF:

0.0000315

AC:

AN:

697310

Other (OTH)

AF:

0.0000529

AC:

AN:

37838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.000162

AC:

AN:

74198

Hom.:

Cov.:

AF XY:

0.000265

AC XY:

AN XY:

33964

show subpopulations

African (AFR)

AF:

0.000332

AC:

AN:

18078

American (AMR)

AF:

0.000153

AC:

AN:

6544

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2212

East Asian (EAS)

AF:

0.00

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:

0.00

AC:

AN:

102

European-Non Finnish (NFE)

AF:

0.000128

AC:

AN:

39032

Other (OTH)

AF:

0.00

AC:

AN:

994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.15

Splicing

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

Publications

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1-151760903-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

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