chr1-151760903-C-CAAAAAAAAAAAAAAAAAA

Position:

• chr1-151760903-C-CAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_031420.4(MRPL9):​c.589-5_589-4insTTTTTTTTTTTTTTTTTT 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 0.0012 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00081 (5 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 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPL9	NM_031420.4	c.589-5_589-4insTTTTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000368830.8	NP_113608.1
MRPL9	NM_001300733.2	c.487-5_487-4insTTTTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NP_001287662.1
MRPL9	NR_125331.2	n.646-5_646-4insTTTTTTTTTTTTTTTTTT		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_589-4insTTTTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_031420.4	ENSP00000357823	P1

Frequencies

GnomAD3 genomes AF: 0.00119 AC: 88 AN: 74188 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00366

Gnomad AMR AF: 0.000764

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000997

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00123

Gnomad OTH AF: 0.00101

GnomAD4 exome AF: 0.000812 AC: 714 AN: 878800 Hom.: 5 Cov.: 0 AF XY: 0.000859 AC XY: 375 AN XY: 436542

Gnomad4 AFR exome AF: 0.000506

Gnomad4 AMR exome AF: 0.000378

Gnomad4 ASJ exome AF: 0.00104

Gnomad4 EAS exome AF: 0.000306

Gnomad4 SAS exome AF: 0.000483

Gnomad4 FIN exome AF: 0.00107

Gnomad4 NFE exome AF: 0.000844

Gnomad4 OTH exome AF: 0.00111

GnomAD4 genome AF: 0.00119 AC: 88 AN: 74182 Hom.: 1 Cov.: 0 AF XY: 0.000972 AC XY: 33 AN XY: 33954

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.000764

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000997

Gnomad4 NFE AF: 0.00123

Gnomad4 OTH AF: 0.00101

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;