17-75262004-GGC-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_015971.4(MRPS7):c.83+23_83+24delCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 1,557,946 control chromosomes in the GnomAD database, including 544,674 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 49031 hom., cov: 0)

Exomes 𝑓: 0.84 ( 495643 hom. )

Consequence

MRPS7
NM_015971.4 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.171

Publications

3 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 17-75262004-GGC-G is Benign according to our data. Variant chr17-75262004-GGC-G is described in ClinVar as Benign. ClinVar VariationId is 1263999.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015971.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRPS7	NM_015971.4	MANE Select	c.83+23_83+24delCG	intron	N/A	NP_057055.2	Q9Y2R9
GGA3	NM_001172703.3		c.-177+276_-177+277delGC	intron	N/A	NP_001166174.1	Q9NZ52-4
GGA3	NM_001172704.3		c.-228+276_-228+277delGC	intron	N/A	NP_001166175.1	Q9NZ52-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRPS7	ENST00000245539.11	TSL:1 MANE Select	c.83+23_83+24delCG	intron	N/A	ENSP00000245539.6	Q9Y2R9
MRPS7	ENST00000579002.5	TSL:2	c.-321_-320delCG	5_prime_UTR	Exon 1 of 4	ENSP00000463683.1	J3QLS3
GGA3	ENST00000582717.5	TSL:2	c.-177+276_-177+277delGC	intron	N/A	ENSP00000462081.1	Q9NZ52-4

Frequencies

GnomAD3 genomes

AF:

0.812

AC:

121479

AN:

149518

Hom.:

49009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.728

Gnomad AMI

AF:

0.842

Gnomad AMR

AF:

0.850

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.936

Gnomad SAS

AF:

0.914

Gnomad FIN

AF:

0.901

Gnomad MID

AF:

0.761

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.789

GnomAD2 exomes

AF:

0.849

AC:

192256

AN:

226428

AF XY:

0.850

show subpopulations

Gnomad AFR exome

AF:

0.722

Gnomad AMR exome

AF:

0.893

Gnomad ASJ exome

AF:

0.749

Gnomad EAS exome

AF:

0.929

Gnomad FIN exome

AF:

0.899

Gnomad NFE exome

AF:

0.825

Gnomad OTH exome

AF:

0.825

GnomAD4 exome

AF:

0.845

AC:

1189657

AN:

1408318

Hom.:

495643

AF XY:

0.846

AC XY:

593846

AN XY:

701570

show subpopulations

African (AFR)

AF:

0.698

AC:

22866

AN:

32772

American (AMR)

AF:

0.893

AC:

39116

AN:

43798

Ashkenazi Jewish (ASJ)

AF:

0.754

AC:

18962

AN:

25138

East Asian (EAS)

AF:

0.943

AC:

37054

AN:

39286

South Asian (SAS)

AF:

0.914

AC:

77457

AN:

84766

European-Finnish (FIN)

AF:

0.895

AC:

37576

AN:

42002

Middle Eastern (MID)

AF:

0.757

AC:

4100

AN:

5416

European-Non Finnish (NFE)

AF:

0.839

AC:

903475

AN:

1076396

Other (OTH)

AF:

0.835

AC:

49051

AN:

58744

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

10552

21104

31657

42209

52761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20704

41408

62112

82816

103520

<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:

0.812

AC:

121549

AN:

149628

Hom.:

49031

Cov.:

AF XY:

0.819

AC XY:

59944

AN XY:

73164

show subpopulations

African (AFR)

AF:

0.728

AC:

28870

AN:

39676

American (AMR)

AF:

0.850

AC:

12907

AN:

15184

Ashkenazi Jewish (ASJ)

AF:

0.742

AC:

2526

AN:

3406

East Asian (EAS)

AF:

0.936

AC:

4817

AN:

5146

South Asian (SAS)

AF:

0.915

AC:

4397

AN:

4808

European-Finnish (FIN)

AF:

0.901

AC:

9516

AN:

10562

Middle Eastern (MID)

AF:

0.747

AC:

215

AN:

288

European-Non Finnish (NFE)

AF:

0.827

AC:

55880

AN:

67554

Other (OTH)

AF:

0.790

AC:

1653

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1209

2418

3628

4837

6046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<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:

0.815

Hom.:

6190

Bravo

AF:

0.790

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Combined oxidative phosphorylation deficiency 34 (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.17

Mutation Taster

=300/0

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