rs2271908

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016065.4(MRPS16):c.13+106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 1,490,708 control chromosomes in the GnomAD database, including 6,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.069 ( 619 hom., cov: 32)

Exomes 𝑓: 0.076 ( 5970 hom. )

Consequence

MRPS16
NM_016065.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.43

Publications

5 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 10-73252364-A-G is Benign according to our data. Variant chr10-73252364-A-G is described in ClinVar as Benign. ClinVar VariationId is 1178938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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.13+106T>C	intron	N/A	NP_057149.1	Q9Y3D3-1
MRPS16	NM_001410935.1		c.13+106T>C	intron	N/A	NP_001397864.1	A6ND22
DNAJC9-AS1	NR_038373.1		n.175+3914A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRPS16	ENST00000372945.8	TSL:1 MANE Select	c.13+106T>C	intron	N/A	ENSP00000362036.3	Q9Y3D3-1
DNAJC9-AS1	ENST00000440197.2	TSL:1	n.182+3914A>G	intron	N/A
MRPS16	ENST00000372940.3	TSL:2	c.13+106T>C	intron	N/A	ENSP00000362031.3	A6ND22

Frequencies

GnomAD3 genomes

AF:

0.0691

AC:

10516

AN:

152164

Hom.:

620

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0433

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0715

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.0415

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0590

Gnomad OTH

AF:

0.0627

GnomAD4 exome

AF:

0.0765

AC:

102327

AN:

1338426

Hom.:

5970

Cov.:

AF XY:

0.0808

AC XY:

54055

AN XY:

668998

show subpopulations

African (AFR)

AF:

0.0423

AC:

1307

AN:

30882

American (AMR)

AF:

0.0764

AC:

3142

AN:

41124

Ashkenazi Jewish (ASJ)

AF:

0.0950

AC:

2373

AN:

24968

East Asian (EAS)

AF:

0.285

AC:

10779

AN:

37806

South Asian (SAS)

AF:

0.214

AC:

17365

AN:

81246

European-Finnish (FIN)

AF:

0.0449

AC:

1921

AN:

42792

Middle Eastern (MID)

AF:

0.0459

AC:

206

AN:

4488

European-Non Finnish (NFE)

AF:

0.0595

AC:

60631

AN:

1018764

Other (OTH)

AF:

0.0817

AC:

4603

AN:

56356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

4917

9835

14752

19670

24587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2466

4932

7398

9864

12330

<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:

0.0691

AC:

10527

AN:

152282

Hom.:

619

Cov.:

AF XY:

0.0718

AC XY:

5345

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.0433

AC:

1800

AN:

41562

American (AMR)

AF:

0.0715

AC:

1095

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0922

AC:

320

AN:

3472

East Asian (EAS)

AF:

0.304

AC:

1567

AN:

5160

South Asian (SAS)

AF:

0.217

AC:

1048

AN:

4828

European-Finnish (FIN)

AF:

0.0415

AC:

441

AN:

10614

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0590

AC:

4013

AN:

68024

Other (OTH)

AF:

0.0658

AC:

139

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

501

1002

1503

2004

2505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0629

Hom.:

Bravo

AF:

0.0679

Asia WGS

AF:

0.240

AC:

834

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.60

(source)

DANN

Benign

0.71

PhyloP100

-1.4

PromoterAI

0.046

Neutral

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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