Variant chr10-73250839-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016065.4(MRPS16):c.*13T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,613,254 control chromosomes in the GnomAD database, including 842 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 418 hom., cov: 32)

Exomes 𝑓: 0.0072 ( 424 hom. )

Consequence

MRPS16
NM_016065.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.728

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 10-73250839-A-G is Benign according to our data. Variant chr10-73250839-A-G is described in ClinVar as [Benign]. Clinvar id is 1291206.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
MRPS16	NM_016065.4 linkuse as main transcript	c.*13T>C	3_prime_UTR_variant	3/3	ENST00000372945.8
DNAJC9-AS1	NR_038373.1 linkuse as main transcript	n.175+2389A>G	intron_variant, non_coding_transcript_variant
MRPS16	XM_047425263.1 linkuse as main transcript	c.*13T>C	3_prime_UTR_variant	3/3
MRPS16	NM_001410935.1 linkuse as main transcript	c.274+924T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPS16	ENST00000372945.8 linkuse as main transcript	c.*13T>C		3_prime_UTR_variant	3/3	1	NM_016065.4	P1	Q9Y3D3-1
DNAJC9-AS1	ENST00000440197.2 linkuse as main transcript	n.182+2389A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0424

AC:

6456

AN:

152130

Hom.:

418

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0154

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00412

Gnomad OTH

AF:

0.0225

GnomAD3 exomes

AF:

0.0130

AC:

3255

AN:

251258

Hom.:

194

AF XY:

0.0102

AC XY:

1384

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.147

Gnomad AMR exome

AF:

0.00604

Gnomad ASJ exome

AF:

0.000893

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.00186

Gnomad FIN exome

AF:

0.00219

Gnomad NFE exome

AF:

0.00438

Gnomad OTH exome

AF:

0.00587

GnomAD4 exome

AF:

0.00715

AC:

10451

AN:

1461006

Hom.:

424

Cov.:

AF XY:

0.00656

AC XY:

4765

AN XY:

726846

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.00662

Gnomad4 ASJ exome

AF:

0.000459

Gnomad4 EAS exome

AF:

0.000756

Gnomad4 SAS exome

AF:

0.00183

Gnomad4 FIN exome

AF:

0.00213

Gnomad4 NFE exome

AF:

0.00371

Gnomad4 OTH exome

AF:

0.0123

GnomAD4 genome

AF:

0.0425

AC:

6465

AN:

152248

Hom.:

418

Cov.:

AF XY:

0.0404

AC XY:

3009

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.0154

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00412

Gnomad4 OTH

AF:

0.0222

Alfa

AF:

0.0316

Hom.:

Bravo

AF:

0.0478

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.94

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over