rs3792252

Variant summary

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

The ENST00000296102.8(MRPL33):​c.41+372G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,076 control chromosomes in the GnomAD database, including 34,540 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 0.67 ( 34540 hom., cov: 32)

Consequence

MRPL33
ENST00000296102.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.332
Variant links:
Genes affected
MRPL33 (HGNC:14487): (mitochondrial ribosomal protein L33) 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. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MRPL33NM_004891.4 linkuse as main transcriptc.41+372G>A intron_variant ENST00000296102.8 NP_004882.1
MRPL33NM_145330.3 linkuse as main transcriptc.41+372G>A intron_variant NP_663303.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MRPL33ENST00000296102.8 linkuse as main transcriptc.41+372G>A intron_variant 1 NM_004891.4 ENSP00000296102 P1O75394-1

Frequencies

GnomAD3 genomes
AF:
0.666
AC:
101146
AN:
151958
Hom.:
34539
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.578
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.576
Gnomad ASJ
AF:
0.754
Gnomad EAS
AF:
0.415
Gnomad SAS
AF:
0.677
Gnomad FIN
AF:
0.698
Gnomad MID
AF:
0.782
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.685
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.665
AC:
101182
AN:
152076
Hom.:
34540
Cov.:
32
AF XY:
0.660
AC XY:
49097
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.577
Gnomad4 AMR
AF:
0.576
Gnomad4 ASJ
AF:
0.754
Gnomad4 EAS
AF:
0.415
Gnomad4 SAS
AF:
0.677
Gnomad4 FIN
AF:
0.698
Gnomad4 NFE
AF:
0.748
Gnomad4 OTH
AF:
0.687
Alfa
AF:
0.728
Hom.:
86590
Bravo
AF:
0.647
Asia WGS
AF:
0.529
AC:
1842
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
7.6
DANN
Benign
0.32

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.

Other links and lift over

dbSNP: rs3792252; hg19: chr2-27995931; API