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3-131462637-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_007208.4(MRPL3):c.*86C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,287,404 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 4 hom. )

Consequence

MRPL3
NM_007208.4 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0430
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 3-131462637-G-A is Benign according to our data. Variant chr3-131462637-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1193072.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00681 (1036/152238) while in subpopulation AFR AF= 0.0239 (991/41534). AF 95% confidence interval is 0.0226. There are 16 homozygotes in gnomad4. There are 509 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
High Homozygotes in GnomAd at 16 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MRPL3NM_007208.4 linkuse as main transcriptc.*86C>T 3_prime_UTR_variant 10/10 ENST00000264995.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MRPL3ENST00000264995.8 linkuse as main transcriptc.*86C>T 3_prime_UTR_variant 10/101 NM_007208.4 P1
MRPL3ENST00000425847.6 linkuse as main transcriptc.*86C>T 3_prime_UTR_variant 11/112
MRPL3ENST00000511168.5 linkuse as main transcriptc.*86C>T 3_prime_UTR_variant 10/102
MRPL3ENST00000510043.1 linkuse as main transcriptn.557C>T non_coding_transcript_exon_variant 4/42

Frequencies

GnomAD3 genomes
AF:
0.00680
AC:
1035
AN:
152120
Hom.:
16
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0239
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00170
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00621
GnomAD4 exome
AF:
0.000630
AC:
715
AN:
1135166
Hom.:
4
Cov.:
14
AF XY:
0.000571
AC XY:
321
AN XY:
562408
show subpopulations
Gnomad4 AFR exome
AF:
0.0231
Gnomad4 AMR exome
AF:
0.000729
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000110
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000160
Gnomad4 OTH exome
AF:
0.00163
GnomAD4 genome
AF:
0.00681
AC:
1036
AN:
152238
Hom.:
16
Cov.:
32
AF XY:
0.00684
AC XY:
509
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0239
Gnomad4 AMR
AF:
0.00170
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00615
Alfa
AF:
0.00492
Hom.:
1
Bravo
AF:
0.00753
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJan 28, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
3.6
Dann
Benign
0.75
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs143594337; hg19: chr3-131181481; API