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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_031420.4(MRPL9):c.589-5_589-4insTTTTTTTTTTTTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00026 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0024 ( 11 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 Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 11 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.000256

AC:

AN:

74202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000111

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:

0.000410

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00244

AC:

2138

AN:

876744

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

1108

AN XY:

435514

show subpopulations

Gnomad4 AFR exome

AF:

0.000732

Gnomad4 AMR exome

AF:

0.000832

Gnomad4 ASJ exome

AF:

0.00305

Gnomad4 EAS exome

AF:

0.000443

Gnomad4 SAS exome

AF:

0.00157

Gnomad4 FIN exome

AF:

0.00346

Gnomad4 NFE exome

AF:

0.00260

Gnomad4 OTH exome

AF:

0.00250

GnomAD4 genome

AF:

0.000256

AC:

AN:

74196

Hom.:

Cov.:

AF XY:

0.000177

AC XY:

AN XY:

33962

show subpopulations

Gnomad4 AFR

AF:

0.000111

Gnomad4 AMR

AF:

0.000153

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000410

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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