1-151760903-CAAAAAAAAAA-CAAAAAAAAA

Position:

• chr1-151760903-CAAAAAAAAAA-CAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. 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 0.0022 (1 hom., cov: 0)
  • Exomes 𝑓: 0.14 (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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL9	NM_031420.4	c.589-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000368830.8
MRPL9	NM_001300733.2	c.487-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
MRPL9	NR_125331.2	n.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	c.589-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031420.4	P1

Frequencies

GnomAD3 genomes AF: 0.00220 AC: 163 AN: 74198 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00532

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00199

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000377

Gnomad SAS AF: 0.00583

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000410

Gnomad OTH AF: 0.00203

GnomAD4 exome AF: 0.143 AC: 121890 AN: 852606 Hom.: 0 Cov.: 0 AF XY: 0.143 AC XY: 60367 AN XY: 423162

Gnomad4 AFR exome AF: 0.0920

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.152

Gnomad4 SAS exome AF: 0.149

Gnomad4 FIN exome AF: 0.126

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.00221 AC: 164 AN: 74192 Hom.: 1 Cov.: 0 AF XY: 0.00224 AC XY: 76 AN XY: 33962

Gnomad4 AFR AF: 0.00537

Gnomad4 AMR AF: 0.00199

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000379

Gnomad4 SAS AF: 0.00587

Gnomad4 FIN AF: 0.0115

Gnomad4 NFE AF: 0.000410

Gnomad4 OTH AF: 0.00201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs755031728; hg19: chr1-151733379;