Variant 1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAA 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.589-16_589-5dupTTTTTTTTTTTT variant causes a splice region, 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 0.000081 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00064 ( 4 hom. )

Consequence

MRPL9
NM_031420.4 splice_region, 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 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
MRPL9	NM_031420.4 link	c.589-16_589-5dupTTTTTTTTTTTT	splice_region_variant, intron_variant	ENST00000368830.8	NP_113608.1	Q9BYD2
MRPL9	NM_001300733.2 link	c.487-16_487-5dupTTTTTTTTTTTT	splice_region_variant, intron_variant		NP_001287662.1	Q9BYD2Q5SZR1
MRPL9	NR_125331.2 link	n.646-16_646-5dupTTTTTTTTTTTT	splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL9	ENST00000368830.8 link	c.589-16_589-5dupTTTTTTTTTTTT		splice_region_variant, intron_variant		1	NM_031420.4	ENSP00000357823.3		Q9BYD2

Frequencies

GnomAD3 genomes

AF:

0.0000809

AC:

AN:

74200

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:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000154

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000637

AC:

560

AN:

878874

Hom.:

Cov.:

AF XY:

0.000639

AC XY:

279

AN XY:

436610

show subpopulations

Gnomad4 AFR exome

AF:

0.000225

Gnomad4 AMR exome

AF:

0.000378

Gnomad4 ASJ exome

AF:

0.00163

Gnomad4 EAS exome

AF:

0.000238

Gnomad4 SAS exome

AF:

0.000621

Gnomad4 FIN exome

AF:

0.000861

Gnomad4 NFE exome

AF:

0.000647

Gnomad4 OTH exome

AF:

0.000582

GnomAD4 genome

AF:

0.0000809

AC:

AN:

74200

Hom.:

Cov.:

AF XY:

0.0000589

AC XY:

AN XY:

33956

show subpopulations

Gnomad4 AFR

AF:

0.00

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:

0.000154

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