Variant rs2271908 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.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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
MRPS16	NM_016065.4 linkuse as main transcript	c.13+106T>C	intron_variant		ENST00000372945.8
DNAJC9-AS1	NR_038373.1 linkuse as main transcript	n.175+3914A>G	intron_variant, non_coding_transcript_variant
MRPS16	XM_047425263.1 linkuse as main transcript	c.-134T>C	5_prime_UTR_variant	1/3
MRPS16	NM_001410935.1 linkuse as main transcript	c.13+106T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPS16	ENST00000372945.8 linkuse as main transcript	c.13+106T>C		intron_variant		1	NM_016065.4	P1	Q9Y3D3-1
DNAJC9-AS1	ENST00000440197.2 linkuse as main transcript	n.182+3914A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR exome

AF:

0.0423

Gnomad4 AMR exome

AF:

0.0764

Gnomad4 ASJ exome

AF:

0.0950

Gnomad4 EAS exome

AF:

0.285

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.0449

Gnomad4 NFE exome

AF:

0.0595

Gnomad4 OTH exome

AF:

0.0817

GnomAD4 genome

AF:

0.0691

AC:

10527

AN:

152282

Hom.:

619

Cov.:

AF XY:

0.0718

AC XY:

5345

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0433

Gnomad4 AMR

AF:

0.0715

Gnomad4 ASJ

AF:

0.0922

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.0415

Gnomad4 NFE

AF:

0.0590

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0632

Hom.:

Bravo

AF:

0.0679

Asia WGS

AF:

0.240

AC:

834

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	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.60

DANN

Benign

0.71

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