Genetic Variant MRPS16:c.*633delT (chr10-73250218-CA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_016065.4(MRPS16):c.*633delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 131,984 control chromosomes in the GnomAD database, including 1,112 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1111 hom., cov: 27)

Exomes 𝑓: 0.25 ( 1 hom. )

Consequence

MRPS16
NM_016065.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0840

Publications

0 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016065.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRPS16	NM_016065.4	MANE Select	c.*633delT	3_prime_UTR	Exon 3 of 3	NP_057149.1	Q9Y3D3-1
MRPS16	NM_001410935.1		c.275-901delT	intron	N/A	NP_001397864.1	A6ND22
DNAJC9-AS1	NR_038373.1		n.175+1784delA	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRPS16	ENST00000372945.8	TSL:1 MANE Select	c.*633delT	3_prime_UTR	Exon 3 of 3	ENSP00000362036.3	Q9Y3D3-1
DNAJC9-AS1	ENST00000440197.2	TSL:1	n.182+1784delA	intron	N/A
MRPS16	ENST00000372940.3	TSL:2	c.275-901delT	intron	N/A	ENSP00000362031.3	A6ND22

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

15440

AN:

131362

Hom.:

1107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.0997

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.0707

Gnomad MID

AF:

0.0571

Gnomad NFE

AF:

0.0685

Gnomad OTH

AF:

0.110

GnomAD4 exome

AF:

0.252

AC:

144

AN:

572

Hom.:

Cov.:

AF XY:

0.253

AC XY:

AN XY:

368

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.240

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.313

AC:

AN:

South Asian (SAS)

AF:

0.382

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.242

AC:

110

AN:

454

Other (OTH)

AF:

0.188

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.118

AC:

15480

AN:

131412

Hom.:

1111

Cov.:

AF XY:

0.120

AC XY:

7598

AN XY:

63086

show subpopulations

African (AFR)

AF:

0.182

AC:

6493

AN:

35706

American (AMR)

AF:

0.0999

AC:

1298

AN:

12998

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

386

AN:

3186

East Asian (EAS)

AF:

0.306

AC:

1392

AN:

4546

South Asian (SAS)

AF:

0.229

AC:

925

AN:

4048

European-Finnish (FIN)

AF:

0.0707

AC:

512

AN:

7244

Middle Eastern (MID)

AF:

0.0586

AC:

AN:

256

European-Non Finnish (NFE)

AF:

0.0685

AC:

4165

AN:

60802

Other (OTH)

AF:

0.114

AC:

204

AN:

1788

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

589

1178

1768

2357

2946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0182

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.084

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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10-73250218-CAAAA-CAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over