3-131469533-T-TAC

Variant names:

• chr3-131469533-T-TAC
• rs3830301
• NM_007208.4:c.816+161_816+162dupGT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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

• Frequency: Genomes: 𝑓 0.032 (84 hom., cov: 0)
• Consequence: MRPL3 NM_007208.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 3-131469533-T-TAC is Benign according to our data. Variant chr3-131469533-T-TAC is described in ClinVar as [Likely_benign]. Clinvar id is 1198044.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0325 (4771/146964) while in subpopulation SAS AF = 0.0514 (238/4626). AF 95% confidence interval is 0.0461. There are 84 homozygotes in GnomAd4. There are 2364 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 84 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL3	NM_007208.4	c.816+161_816+162dupGT		intron_variant	Intron 8 of 9	ENST00000264995.8	NP_009139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL3	ENST00000264995.8	c.816+162_816+163insGT		intron_variant	Intron 8 of 9	1	NM_007208.4	ENSP00000264995.2

Frequencies

GnomAD3 genomes AF: 0.0325 AC: 4768 AN: 146852 Hom.: 83 Cov.: 0

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0831

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0417

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0400

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0303

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

GnomAD4 genome AF: 0.0325 AC: 4771 AN: 146964 Hom.: 84 Cov.: 0 AF XY: 0.0330 AC XY: 2364 AN XY: 71678

Gnomad4 AFR AF: 0.0184 AC: 0.0183532 AN: 0.0183532

Gnomad4 AMR AF: 0.0260 AC: 0.0259687 AN: 0.0259687

Gnomad4 ASJ AF: 0.0417 AC: 0.0417402 AN: 0.0417402

Gnomad4 EAS AF: 0.0385 AC: 0.0384776 AN: 0.0384776

Gnomad4 SAS AF: 0.0514 AC: 0.0514483 AN: 0.0514483

Gnomad4 FIN AF: 0.0367 AC: 0.0367499 AN: 0.0367499

Gnomad4 NFE AF: 0.0389 AC: 0.0388877 AN: 0.0388877

Gnomad4 OTH AF: 0.0305 AC: 0.0305305 AN: 0.0305305

Alfa AF: 0.0349 Hom.: 533

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 15, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism

Splicing

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;