Genetic Variant MRPS16:c.*631_*633delTTT (chr10-73250218-CAAA-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_016065.4(MRPS16):c.*631_*633delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 132,104 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 27)

Exomes 𝑓: 0.016 ( 0 hom. )

Consequence

MRPS16
NM_016065.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0840

Variant links:

Genes affected

MRPS16 (HGNC:14048): (mitochondrial ribosomal protein S16) 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 28S subunit protein that belongs to the ribosomal protein S16P family. The encoded protein is one of the most highly conserved ribosomal proteins between mammalian and yeast mitochondria. Three pseudogenes (located at 8q21.3, 20q13.32, 22q12-q13.1) for this gene have been described. [provided by RefSeq, Jul 2008]

MRPS16 links:

DNAJC9-AS1 (HGNC:31432): (DNAJC9 and MRPS16 antisense RNA 1)

DNAJC9-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MRPS16	NM_016065.4 link	c.631_633delTTT	3_prime_UTR_variant	Exon 3 of 3	ENST00000372945.8	NP_057149.1	Q9Y3D3-1
MRPS16	XM_047425263.1 link	c.631_633delTTT	3_prime_UTR_variant	Exon 3 of 3		XP_047281219.1
MRPS16	NM_001410935.1 link	c.275-903_275-901delTTT	intron_variant	Intron 2 of 2		NP_001397864.1
DNAJC9-AS1	NR_038373.1 link	n.175+1782_175+1784delAAA	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MRPS16	ENST00000372945 link	c.631_633delTTT	3_prime_UTR_variant	Exon 3 of 3	1	NM_016065.4	ENSP00000362036.3	Q9Y3D3-1
DNAJC9-AS1	ENST00000440197.2 link	n.182+1782_182+1784delAAA	intron_variant	Intron 2 of 3	1
MRPS16	ENST00000372940.3 link	c.275-903_275-901delTTT	intron_variant	Intron 2 of 2	2		ENSP00000362031.3	A6ND22
MRPS16	ENST00000479005.1 link	n.1202_1204delTTT	non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0000532

AC:

AN:

131530

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000275

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0157

AC:

AN:

574

Hom.:

AF XY:

0.0135

AC XY:

AN XY:

370

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0625

Gnomad4 SAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0154

Gnomad4 OTH exome

AF:

0.0625

GnomAD4 genome

AF:

0.0000532

AC:

AN:

131530

Hom.:

Cov.:

AF XY:

0.0000317

AC XY:

AN XY:

63096

show subpopulations

Gnomad4 AFR

AF:

0.000140

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000275

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

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.

10-73250218-CAAAA-CA

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