Variant 17-75262005-GC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015971.4(MRPS7):c.83+23del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 559 hom., cov: 0)

Exomes 𝑓: 0.017 ( 475 hom. )

Consequence

MRPS7
NM_015971.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

MRPS7 (HGNC:14499): (mitochondrial ribosomal protein S7) 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. In the prokaryotic ribosome, the comparable protein is thought to play an essential role in organizing the 3' domain of the 16 S rRNA in the vicinity of the P- and A-sites. Pseudogenes corresponding to this gene are found on chromosomes 8p and 12p. [provided by RefSeq, Jul 2008]

MRPS7 links:

GGA3 (HGNC:17079): (golgi associated, gamma adaptin ear containing, ARF binding protein 3) This gene encodes a member of the Golgi-localized, gamma adaptin ear-containing, ARF-binding (GGA) family. This family includes ubiquitous coat proteins that regulate the trafficking of proteins between the trans-Golgi network and the lysosome. These proteins share an amino-terminal VHS domain which mediates sorting of the mannose 6-phosphate receptors at the trans-Golgi network. They also contain a carboxy-terminal region with homology to the ear domain of gamma-adaptins. Multiple alternatively spliced transcript variants have been identified in this gene. [provided by RefSeq, Feb 2010]

GGA3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-75262005-GC-G is Benign according to our data. Variant chr17-75262005-GC-G is described in ClinVar as [Benign]. Clinvar id is 1231509.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
MRPS7	NM_015971.4 linkuse as main transcript	c.83+23del	intron_variant	ENST00000245539.11	NP_057055.2
GGA3	NM_001172703.3 linkuse as main transcript	c.-177+276del	intron_variant		NP_001166174.1
GGA3	NM_001172704.3 linkuse as main transcript	c.-228+276del	intron_variant		NP_001166175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPS7	ENST00000245539.11 linkuse as main transcript	c.83+23del		intron_variant		1	NM_015971.4	ENSP00000245539	P1

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

7112

AN:

47848

Hom.:

554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0692

Gnomad ASJ

AF:

0.00831

Gnomad EAS

AF:

0.0168

Gnomad SAS

AF:

0.0162

Gnomad FIN

AF:

0.00194

Gnomad MID

AF:

0.0294

Gnomad NFE

AF:

0.00543

Gnomad OTH

AF:

0.0963

GnomAD3 exomes

AF:

0.0132

AC:

3021

AN:

228714

Hom.:

150

AF XY:

0.0105

AC XY:

1321

AN XY:

126046

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.0115

Gnomad ASJ exome

AF:

0.00395

Gnomad EAS exome

AF:

0.00187

Gnomad SAS exome

AF:

0.00295

Gnomad FIN exome

AF:

0.000891

Gnomad NFE exome

AF:

0.00160

Gnomad OTH exome

AF:

0.00813

GnomAD4 exome

AF:

0.0171

AC:

8825

AN:

517564

Hom.:

475

Cov.:

AF XY:

0.0155

AC XY:

3906

AN XY:

252656

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.0638

Gnomad4 ASJ exome

AF:

0.00953

Gnomad4 EAS exome

AF:

0.0129

Gnomad4 SAS exome

AF:

0.0126

Gnomad4 FIN exome

AF:

0.0141

Gnomad4 NFE exome

AF:

0.00325

Gnomad4 OTH exome

AF:

0.0391

GnomAD4 genome

AF:

0.149

AC:

7133

AN:

47908

Hom.:

559

Cov.:

AF XY:

0.148

AC XY:

3357

AN XY:

22712

show subpopulations

Gnomad4 AFR

AF:

0.422

Gnomad4 AMR

AF:

0.0692

Gnomad4 ASJ

AF:

0.00831

Gnomad4 EAS

AF:

0.0154

Gnomad4 SAS

AF:

0.0162

Gnomad4 FIN

AF:

0.00194

Gnomad4 NFE

AF:

0.00543

Gnomad4 OTH

AF:

0.0995

Alfa

AF:

0.00221

Hom.:

Bravo

AF:

0.0545

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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