Variant rs2018198 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_016065.4(MRPS16):c.*1503A>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 0.0788 in 1,541,096 control chromosomes in the GnomAD database, including 7,092 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 0.092 ( 923 hom., cov: 32)

Exomes 𝑓: 0.077 ( 6169 hom. )

Consequence

MRPS16
NM_016065.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

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 Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MRPS16	NM_016065.4 link	c.*1503A>T	3_prime_UTR_variant	Exon 3 of 3	ENST00000372945.8	NP_057149.1	Q9Y3D3-1
MRPS16	XM_047425263.1 link	c.*1503A>T	3_prime_UTR_variant	Exon 3 of 3		XP_047281219.1
MRPS16	NM_001410935.1 link	c.275-31A>T	intron_variant	Intron 2 of 2		NP_001397864.1
DNAJC9-AS1	NR_038373.1 link	n.175+899T>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS16	ENST00000372945.8 link	c.*1503A>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_016065.4	ENSP00000362036.3		Q9Y3D3-1

Frequencies

GnomAD3 genomes

AF:

0.0917

AC:

13947

AN:

152062

Hom.:

907

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0803

Gnomad ASJ

AF:

0.0973

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.0416

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0597

Gnomad OTH

AF:

0.0823

GnomAD3 exomes

AF:

0.108

AC:

16280

AN:

151346

Hom.:

1374

AF XY:

0.114

AC XY:

9254

AN XY:

81226

show subpopulations

Gnomad AFR exome

AF:

0.124

Gnomad AMR exome

AF:

0.0810

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.297

Gnomad SAS exome

AF:

0.216

Gnomad FIN exome

AF:

0.0439

Gnomad NFE exome

AF:

0.0605

Gnomad OTH exome

AF:

0.0872

GnomAD4 exome

AF:

0.0773

AC:

107393

AN:

1388916

Hom.:

6169

Cov.:

AF XY:

0.0812

AC XY:

55700

AN XY:

685544

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.0816

Gnomad4 ASJ exome

AF:

0.0992

Gnomad4 EAS exome

AF:

0.284

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.0454

Gnomad4 NFE exome

AF:

0.0595

Gnomad4 OTH exome

AF:

0.0882

GnomAD4 genome

AF:

0.0921

AC:

14010

AN:

152180

Hom.:

923

Cov.:

AF XY:

0.0941

AC XY:

7007

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0803

Gnomad4 ASJ

AF:

0.0973

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.0416

Gnomad4 NFE

AF:

0.0597

Gnomad4 OTH

AF:

0.0852

Alfa

AF:

0.0472

Hom.:

Bravo

AF:

0.0936

Asia WGS

AF:

0.249

AC:

866

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.4

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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.

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