1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Position:

• chr1-151760903-CAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-5_589-4insTTTTTTTTTTTTTTTTTTT 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 0.00036 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00038 (4 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.000377 AC: 28 AN: 74202 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000222

Gnomad AMI AF: 0.00183

Gnomad AMR AF: 0.000611

Gnomad ASJ AF: 0.000452

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00893

Gnomad NFE AF: 0.000435

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000375 AC: 330 AN: 879288 Hom.: 4 Cov.: 0 AF XY: 0.000408 AC XY: 178 AN XY: 436800

Gnomad4 AFR exome AF: 0.000563

Gnomad4 AMR exome AF: 0.000151

Gnomad4 ASJ exome AF: 0.000888

Gnomad4 EAS exome AF: 0.0000681

Gnomad4 SAS exome AF: 0.000529

Gnomad4 FIN exome AF: 0.000328

Gnomad4 NFE exome AF: 0.000364

Gnomad4 OTH exome AF: 0.000423

GnomAD4 genome AF: 0.000364 AC: 27 AN: 74196 Hom.: 1 Cov.: 0 AF XY: 0.000353 AC XY: 12 AN XY: 33962

Gnomad4 AFR AF: 0.000221

Gnomad4 AMR AF: 0.000611

Gnomad4 ASJ AF: 0.000452

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000436

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;