Variant 16-1772158-T-C 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 ENST00000397375.7(MRPS34):c.*63A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,500,538 control chromosomes in the GnomAD database, including 13,848 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1040 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12808 hom. )

Consequence

MRPS34
ENST00000397375.7 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.46

Variant links:

Genes affected

MRPS34 (HGNC:16618): (mitochondrial ribosomal protein S34) 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MRPS34 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 16-1772158-T-C is Benign according to our data. Variant chr16-1772158-T-C is described in ClinVar as [Benign]. Clinvar id is 1221216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPS34	NM_023936.2 linkuse as main transcript	c.*63A>G		3_prime_UTR_variant	3/3	ENST00000397375.7	NP_076425.1
MRPS34	NM_001300900.2 linkuse as main transcript	c.*63A>G		3_prime_UTR_variant	3/3		NP_001287829.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
MRPS34	ENST00000397375.7 linkuse as main transcript	c.*63A>G	3_prime_UTR_variant	3/3	1	NM_023936.2	ENSP00000380531	P1
MRPS34	ENST00000177742.7 linkuse as main transcript	c.*63A>G	3_prime_UTR_variant	3/3	1		ENSP00000177742
MRPS34	ENST00000569585.1 linkuse as main transcript	n.451A>G	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16466

AN:

152078

Hom.:

1043

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0485

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0847

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.103

GnomAD4 exome

AF:

0.129

AC:

174407

AN:

1348342

Hom.:

12808

Cov.:

AF XY:

0.132

AC XY:

88020

AN XY:

667910

show subpopulations

Gnomad4 AFR exome

AF:

0.0459

Gnomad4 AMR exome

AF:

0.0807

Gnomad4 ASJ exome

AF:

0.0908

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.197

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.108

AC:

16455

AN:

152196

Hom.:

1040

Cov.:

AF XY:

0.111

AC XY:

8231

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0485

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.0847

Gnomad4 EAS

AF:

0.247

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.100

Alfa

AF:

0.114

Hom.:

1003

Bravo

AF:

0.100

Asia WGS

AF:

0.195

AC:

677

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	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.8

DANN

Benign

0.57

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