rs200739528

Variant names:

• chr17-75262003-CG-C
• rs200739528
• NM_015971.4:c.83+22delG

Your query was ambiguous. Multiple possible variants found:

• chr17-75262003-CG-C
• chr17-75262003-CG-CGG
• chr17-75262003-CG-CGGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

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]

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS7	NM_015971.4	c.83+22delG		intron_variant	Intron 1 of 4	ENST00000245539.11	NP_057055.2
GGA3	NM_001172703.3	c.-177+278delC		intron_variant	Intron 1 of 16		NP_001166174.1
GGA3	NM_001172704.3	c.-228+278delC		intron_variant	Intron 1 of 15		NP_001166175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS7	ENST00000245539.11	c.83+22delG		intron_variant	Intron 1 of 4	1	NM_015971.4	ENSP00000245539.6

Frequencies

GnomAD3 genomes AF: 0.000257 AC: 10 AN: 38902 Hom.: 0 Cov.: 31

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

GnomAD3 exomes AF: 0.000402 AC: 23 AN: 57250 Hom.: 0 AF XY: 0.000500 AC XY: 16 AN XY: 32022

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 SAS 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: 49 AN: 1411596 Hom.: 0 Cov.: 44 AF XY: 0.0000442 AC XY: 31 AN XY: 701644

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000463

Gnomad4 ASJ exome AF: 0.0000787

Gnomad4 EAS exome AF: 0.0000529

Gnomad4 SAS exome AF: 0.0000120

Gnomad4 FIN exome AF: 0.000144

Gnomad4 NFE exome AF: 0.0000323

Gnomad4 OTH exome AF: 0.0000171

GnomAD4 genome AF: 0.000257 AC: 10 AN: 38958 Hom.: 0 Cov.: 31 AF XY: 0.000218 AC XY: 4 AN XY: 18320

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.000295

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00161

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000302

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs200739528; hg19: chr17-73258084;