Variant rs4764600 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016497.4(MRPL51):c.190+48G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,520,864 control chromosomes in the GnomAD database, including 68,492 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 10343 hom., cov: 32)

Exomes 𝑓: 0.29 ( 58149 hom. )

Consequence

MRPL51
NM_016497.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.74

Variant links:

Genes affected

MRPL51 (HGNC:14044): (mitochondrial ribosomal protein L51) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Pseudogenes corresponding to this gene are found on chromosomes 4p and 21q. [provided by RefSeq, Jul 2008]

MRPL51 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPL51	NM_016497.4 linkuse as main transcript	c.190+48G>C		intron_variant		ENST00000229238.5	NP_057581.2	Q4U2R6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL51	ENST00000229238.5 linkuse as main transcript	c.190+48G>C		intron_variant		1	NM_016497.4	ENSP00000229238.3		Q4U2R6

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53641

AN:

151812

Hom.:

10330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.416

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.374

GnomAD3 exomes

AF:

0.316

AC:

78865

AN:

249690

Hom.:

13307

AF XY:

0.309

AC XY:

41759

AN XY:

135182

show subpopulations

Gnomad AFR exome

AF:

0.521

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.423

Gnomad EAS exome

AF:

0.227

Gnomad SAS exome

AF:

0.264

Gnomad FIN exome

AF:

0.256

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.324

GnomAD4 exome

AF:

0.285

AC:

390712

AN:

1368934

Hom.:

58149

Cov.:

AF XY:

0.285

AC XY:

195375

AN XY:

685604

show subpopulations

Gnomad4 AFR exome

AF:

0.531

Gnomad4 AMR exome

AF:

0.410

Gnomad4 ASJ exome

AF:

0.429

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.264

Gnomad4 FIN exome

AF:

0.261

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.309

GnomAD4 genome

AF:

0.353

AC:

53696

AN:

151930

Hom.:

10343

Cov.:

AF XY:

0.351

AC XY:

26086

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.515

Gnomad4 AMR

AF:

0.361

Gnomad4 ASJ

AF:

0.433

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.370

Alfa

AF:

0.256

Hom.:

947

Bravo

AF:

0.372

Asia WGS

AF:

0.284

AC:

989

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.14

DANN

Benign

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over