1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAA

Position:

• chr1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-5_589-4insTTTTTTTTTTTTTTT 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 0.023 (157 hom., cov: 0)
  • Exomes 𝑓: 0.0036 (14 hom.)
  • Failed GnomAD Quality Control
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL9	NM_031420.4	c.589-5_589-4insTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000368830.8
MRPL9	NM_001300733.2	c.487-5_487-4insTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
MRPL9	NR_125331.2	n.646-5_646-4insTTTTTTTTTTTTTTT		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.589-5_589-4insTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031420.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1679 AN: 74112 Hom.: 157 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00582

Gnomad AMI AF: 0.0311

Gnomad AMR AF: 0.0104

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.00227

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.00399

Gnomad MID AF: 0.00893

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0255

GnomAD4 exome AF: 0.00362 AC: 3166 AN: 875472 Hom.: 14 Cov.: 0 AF XY: 0.00368 AC XY: 1601 AN XY: 434876

Gnomad4 AFR exome AF: 0.00135

Gnomad4 AMR exome AF: 0.00227

Gnomad4 ASJ exome AF: 0.00566

Gnomad4 EAS exome AF: 0.00143

Gnomad4 SAS exome AF: 0.00154

Gnomad4 FIN exome AF: 0.00463

Gnomad4 NFE exome AF: 0.00384

Gnomad4 OTH exome AF: 0.00370

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0227 AC: 1679 AN: 74106 Hom.: 157 Cov.: 0 AF XY: 0.0205 AC XY: 694 AN XY: 33918

Gnomad4 AFR AF: 0.00581

Gnomad4 AMR AF: 0.0104

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.00228

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.00399

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0253

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;