1-151760903-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAA

Variant names:

• chr1-151760903-C-CAAAAAA
• rs755031728
• NM_031420.4:c.589-10_589-5dupTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_031420.4(MRPL9):​c.589-10_589-5dupTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (11 hom., cov: 0)
  • Exomes 𝑓: 0.00059 (1 hom.)
• Consequence: MRPL9 NM_031420.4 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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 -6 ACMG points.

• BP6: Variant 1-151760903-C-CAAAAAA is Benign according to our data. Variant chr1-151760903-C-CAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 3388833.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL9	NM_031420.4	c.589-10_589-5dupTTTTTT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000368830.8	NP_113608.1
MRPL9	NM_001300733.2	c.487-10_487-5dupTTTTTT		splice_region_variant, intron_variant	Intron 4 of 5		NP_001287662.1
MRPL9	NR_125331.2	n.646-10_646-5dupTTTTTT		splice_region_variant, intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL9	ENST00000368830.8	c.589-10_589-5dupTTTTTT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_031420.4	ENSP00000357823.3

Frequencies

GnomAD3 genomes AF: 0.00182 AC: 135 AN: 74192 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.00687

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000764

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: 0.000102

Gnomad OTH AF: 0.00203

GnomAD4 exome AF: 0.000589 AC: 518 AN: 879114 Hom.: 1 Cov.: 0 AF XY: 0.000650 AC XY: 284 AN XY: 436744

Gnomad4 AFR exome AF: 0.00231

Gnomad4 AMR exome AF: 0.00166

Gnomad4 ASJ exome AF: 0.000739

Gnomad4 EAS exome AF: 0.000476

Gnomad4 SAS exome AF: 0.00108

Gnomad4 FIN exome AF: 0.000737

Gnomad4 NFE exome AF: 0.000479

Gnomad4 OTH exome AF: 0.000846

GnomAD4 genome AF: 0.00182 AC: 135 AN: 74184 Hom.: 11 Cov.: 0 AF XY: 0.00183 AC XY: 62 AN XY: 33958

Gnomad4 AFR AF: 0.00686

Gnomad4 AMR AF: 0.000764

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000102

Gnomad4 OTH AF: 0.00201

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MRPL9: BP4, BS2 -

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;