dbSNP rs200739528: MRPS7:c.83+22delG (chr17-75262003-CG-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015971.4(MRPS7):c.83+22delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000407 in 1,450,554 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00026 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

MRPS7
NM_015971.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336

Publications

0 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: Uncertain_significance. The variant received 0 ACMG points.

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+22delG	intron	N/A	NP_057055.2	Q9Y2R9
GGA3	NM_001172703.3		c.-177+278delC	intron	N/A	NP_001166174.1	Q9NZ52-4
GGA3	NM_001172704.3		c.-228+278delC	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+22delG	intron	N/A	ENSP00000245539.6	Q9Y2R9
MRPS7	ENST00000579002.5	TSL:2	c.-322delG	5_prime_UTR	Exon 1 of 4	ENSP00000463683.1	J3QLS3
GGA3	ENST00000582717.5	TSL:2	c.-177+278delC	intron	N/A	ENSP00000462081.1	Q9NZ52-4

Frequencies

GnomAD3 genomes

AF:

0.000257

AC:

AN:

38902

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000194

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000295

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00161

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000302

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000402

AC:

AN:

57250

AF XY:

0.000500

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000255

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00221

Gnomad NFE exome

AF:

0.000509

Gnomad OTH exome

AF:

0.000595

GnomAD4 exome

AF:

0.0000347

AC:

AN:

1411596

Hom.:

Cov.:

AF XY:

0.0000442

AC XY:

AN XY:

701644

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

32764

American (AMR)

AF:

0.0000463

AC:

AN:

43162

Ashkenazi Jewish (ASJ)

AF:

0.0000787

AC:

AN:

25414

East Asian (EAS)

AF:

0.0000529

AC:

AN:

37780

South Asian (SAS)

AF:

0.0000120

AC:

AN:

83060

European-Finnish (FIN)

AF:

0.000144

AC:

AN:

41662

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5588

European-Non Finnish (NFE)

AF:

0.0000323

AC:

AN:

1083550

Other (OTH)

AF:

0.0000171

AC:

AN:

58616

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.406

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.000257

AC:

AN:

38958

Hom.:

Cov.:

AF XY:

0.000218

AC XY:

AN XY:

18320

show subpopulations

African (AFR)

AF:

0.000193

AC:

AN:

10348

American (AMR)

AF:

0.000295

AC:

AN:

3386

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1470

East Asian (EAS)

AF:

0.00

AC:

AN:

550

South Asian (SAS)

AF:

0.00161

AC:

AN:

622

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1778

Middle Eastern (MID)

AF:

0.00

AC:

AN:

114

European-Non Finnish (NFE)

AF:

0.000302

AC:

AN:

19866

Other (OTH)

AF:

0.00

AC:

AN:

594

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.34

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

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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