Variant chr1-151760903-CAAAA-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_031420.4(MRPL9):c.589-8_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 0.00254 in 947,928 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000027 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0028 ( 0 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.93

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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.0000270

AC:

AN:

74202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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:

0.00276

AC:

2410

AN:

873726

Hom.:

AF XY:

0.00277

AC XY:

1204

AN XY:

433954

show subpopulations

Gnomad4 AFR exome

AF:

0.00187

Gnomad4 AMR exome

AF:

0.00351

Gnomad4 ASJ exome

AF:

0.00223

Gnomad4 EAS exome

AF:

0.00164

Gnomad4 SAS exome

AF:

0.00349

Gnomad4 FIN exome

AF:

0.00202

Gnomad4 NFE exome

AF:

0.00281

Gnomad4 OTH exome

AF:

0.00261

GnomAD4 genome

AF:

0.0000270

AC:

AN:

74202

Hom.:

Cov.:

AF XY:

0.0000589

AC XY:

AN XY:

33956

show subpopulations

Gnomad4 AFR

AF:

0.000111

Gnomad4 AMR

AF:

0.00

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

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