Variant 1-151760903-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_031420.4(MRPL9):c.589-5_589-4insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.037 ( 135 hom., cov: 0)

Exomes 𝑓: 0.11 ( 457 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.153

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
MRPL9	NM_031420.4 linkuse as main transcript	c.589-5_589-4insT	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000368830.8
MRPL9	NM_001300733.2 linkuse as main transcript	c.487-5_487-4insT	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
MRPL9	NR_125331.2 linkuse as main transcript	n.646-5_646-4insT	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
MRPL9	ENST00000368830.8 linkuse as main transcript	c.589-5_589-4insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031420.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0366

AC:

2708

AN:

74034

Hom.:

137

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0341

Gnomad AMI

AF:

0.0366

Gnomad AMR

AF:

0.0237

Gnomad ASJ

AF:

0.0186

Gnomad EAS

AF:

0.00831

Gnomad SAS

AF:

0.0667

Gnomad FIN

AF:

0.0249

Gnomad MID

AF:

0.0536

Gnomad NFE

AF:

0.0418

Gnomad OTH

AF:

0.0348

GnomAD4 exome

AF:

0.109

AC:

93895

AN:

858534

Hom.:

457

Cov.:

AF XY:

0.110

AC XY:

46706

AN XY:

426392

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.0930

Gnomad4 EAS exome

AF:

0.0802

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0365

AC:

2703

AN:

74028

Hom.:

135

Cov.:

AF XY:

0.0360

AC XY:

1219

AN XY:

33894

show subpopulations

Gnomad4 AFR

AF:

0.0341

Gnomad4 AMR

AF:

0.0235

Gnomad4 ASJ

AF:

0.0186

Gnomad4 EAS

AF:

0.00835

Gnomad4 SAS

AF:

0.0652

Gnomad4 FIN

AF:

0.0249

Gnomad4 NFE

AF:

0.0418

Gnomad4 OTH

AF:

0.0355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over