1-151760903-C-CAAAAAAAAA

Position:

• chr1-151760903-C-CAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-5_589-4insTTTTTTTTT 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 0.00032 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00016 (0 hom.)
• Consequence: MRPL9 NM_031420.4 splice_region, splice_polypyrimidine_tract, 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL9	ENST00000368830.8	c.589-5_589-4insTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031420.4	ENSP00000357823	P1

Frequencies

GnomAD3 genomes AF: 0.000323 AC: 24 AN: 74200 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00116

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: 0.0000769

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000159 AC: 140 AN: 879594 Hom.: 0 Cov.: 0 AF XY: 0.000174 AC XY: 76 AN XY: 436964

Gnomad4 AFR exome AF: 0.000562

Gnomad4 AMR exome AF: 0.000226

Gnomad4 ASJ exome AF: 0.000369

Gnomad4 EAS exome AF: 0.0000340

Gnomad4 SAS exome AF: 0.000161

Gnomad4 FIN exome AF: 0.0000819

Gnomad4 NFE exome AF: 0.000151

Gnomad4 OTH exome AF: 0.000185

GnomAD4 genome AF: 0.000323 AC: 24 AN: 74194 Hom.: 0 Cov.: 0 AF XY: 0.000353 AC XY: 12 AN XY: 33964

Gnomad4 AFR AF: 0.00116

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: 0.0000769

Gnomad4 OTH AF: 0.00

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;