Variant 3-131468049-CAAAAAA-CAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_007208.4(MRPL3):c.894+40_894+41delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 833,282 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 0)

Exomes 𝑓: 0.026 ( 6 hom. )

Consequence

MRPL3
NM_007208.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.292

Variant links:

Genes affected

MRPL3 (HGNC:10379): (mitochondrial ribosomal protein L3) 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 that belongs to the L3P ribosomal protein family. A pseudogene corresponding to this gene is found on chromosome 13q. [provided by RefSeq, Jul 2008]

MRPL3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL3	NM_007208.4 link	c.894+40_894+41delTT		intron_variant	Intron 9 of 9	ENST00000264995.8	NP_009139.1	P09001

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MRPL3	ENST00000264995.8 link	c.894+40_894+41delTT	intron_variant	Intron 9 of 9	1	NM_007208.4	ENSP00000264995.2	P09001
MRPL3	ENST00000425847.6 link	c.975+40_975+41delTT	intron_variant	Intron 10 of 10	2		ENSP00000398536.2	E7ETU7
MRPL3	ENST00000511168.5 link	c.936+40_936+41delTT	intron_variant	Intron 9 of 9	2		ENSP00000424107.1	H0Y9G6
MRPL3	ENST00000510043.1 link	n.318+40_318+41delTT	intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.00116

AC:

160

AN:

137718

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000437

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00278

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.000220

Gnomad SAS

AF:

0.00382

Gnomad FIN

AF:

0.00211

Gnomad MID

AF:

0.0110

Gnomad NFE

AF:

0.000515

Gnomad OTH

AF:

0.00105

GnomAD3 exomes

AF:

0.0327

AC:

3677

AN:

112418

Hom.:

AF XY:

0.0343

AC XY:

2129

AN XY:

62146

show subpopulations

Gnomad AFR exome

AF:

0.0659

Gnomad AMR exome

AF:

0.0267

Gnomad ASJ exome

AF:

0.0501

Gnomad EAS exome

AF:

0.0164

Gnomad SAS exome

AF:

0.0360

Gnomad FIN exome

AF:

0.0143

Gnomad NFE exome

AF:

0.0336

Gnomad OTH exome

AF:

0.0412

GnomAD4 exome

AF:

0.0260

AC:

18072

AN:

695526

Hom.:

AF XY:

0.0269

AC XY:

9631

AN XY:

357476

show subpopulations

Gnomad4 AFR exome

AF:

0.0652

Gnomad4 AMR exome

AF:

0.0268

Gnomad4 ASJ exome

AF:

0.0351

Gnomad4 EAS exome

AF:

0.0135

Gnomad4 SAS exome

AF:

0.0355

Gnomad4 FIN exome

AF:

0.0178

Gnomad4 NFE exome

AF:

0.0251

Gnomad4 OTH exome

AF:

0.0297

GnomAD4 genome

AF:

0.00116

AC:

160

AN:

137756

Hom.:

Cov.:

AF XY:

0.00133

AC XY:

AN XY:

66680

show subpopulations

Gnomad4 AFR

AF:

0.000436

Gnomad4 AMR

AF:

0.00278

Gnomad4 ASJ

AF:

0.0109

Gnomad4 EAS

AF:

0.000221

Gnomad4 SAS

AF:

0.00384

Gnomad4 FIN

AF:

0.00211

Gnomad4 NFE

AF:

0.000515

Gnomad4 OTH

AF:

0.00156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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