3-131469533-TAC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_007208.4(MRPL3):c.816+161_816+162del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.55 (21722 hom., cov: 0)
• Consequence: MRPL3 NM_007208.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.888

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-131469533-TAC-T is Benign according to our data. Variant chr3-131469533-TAC-T is described in ClinVar as [Benign]. Clinvar id is 1259936.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL3	NM_007208.4	c.816+161_816+162del		intron_variant		ENST00000264995.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPL3	ENST00000264995.8	c.816+161_816+162del		intron_variant		1	NM_007208.4	P1
MRPL3	ENST00000425847.6	c.897+161_897+162del		intron_variant		2
MRPL3	ENST00000511168.5	c.859+161_859+162del		intron_variant		2
MRPL3	ENST00000510043.1	n.240+161_240+162del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 80316 AN: 146404 Hom.: 21713 Cov.: 0

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.557

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.549 AC: 80368 AN: 146514 Hom.: 21722 Cov.: 0 AF XY: 0.543 AC XY: 38779 AN XY: 71420

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.555

Bravo AF: 0.563

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3830301; hg19: chr3-131188377;