rs36039201

Variant names:

• chr17-75262004-GGC-G
• rs36039201
• NM_015971.4:c.83+23_83+24delCG

Your query was ambiguous. Multiple possible variants found:

• chr17-75262004-GGC-G
• chr17-75262004-GGC-GGCGC

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

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

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 0

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

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

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

GnomAD4 genome AF: 0.812 AC: 121549 AN: 149628 Hom.: 49031 Cov.: 0 AF XY: 0.819 AC XY: 59944 AN XY: 73164

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

Alfa AF: 0.815 Hom.: 6190

Bravo AF: 0.790

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Combined oxidative phosphorylation deficiency 34 (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.17
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs36039201; hg19: chr17-73258085;