1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAA

Position:

• chr1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-7_589-5dupTTT 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 0.26 (3078 hom., cov: 0)
  • Exomes 𝑓: 0.074 (249 hom.)
  • Failed GnomAD Quality Control
• Consequence: MRPL9 NM_031420.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPL9	NM_031420.4	c.589-7_589-5dupTTT		splice_region_variant, intron_variant		ENST00000368830.8	NP_113608.1
MRPL9	NM_001300733.2	c.487-7_487-5dupTTT		splice_region_variant, intron_variant			NP_001287662.1
MRPL9	NR_125331.2	n.646-7_646-5dupTTT		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL9	ENST00000368830.8	c.589-7_589-5dupTTT		splice_region_variant, intron_variant		1	NM_031420.4	ENSP00000357823.3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 19234 AN: 73886 Hom.: 3077 Cov.: 0

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.0736 AC: 61867 AN: 840334 Hom.: 249 Cov.: 0 AF XY: 0.0728 AC XY: 30419 AN XY: 417764

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.112

Gnomad4 ASJ exome AF: 0.109

Gnomad4 EAS exome AF: 0.0826

Gnomad4 SAS exome AF: 0.0562

Gnomad4 FIN exome AF: 0.0958

Gnomad4 NFE exome AF: 0.0713

Gnomad4 OTH exome AF: 0.0766

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.260 AC: 19237 AN: 73884 Hom.: 3078 Cov.: 0 AF XY: 0.259 AC XY: 8765 AN XY: 33818

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755031728; hg19: chr1-151733379;