17-75262006-C-A

Variant names:

• chr17-75262006-C-A
• rs62085969
• NM_015971.4:c.83+23C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_015971.4(MRPS7):​c.83+23C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: MRPS7 NM_015971.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

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+23C>A		intron	N/A	NP_057055.2	Q9Y2R9
	GGA3	NM_001172703.3		c.-177+276G>T		intron	N/A	NP_001166174.1	Q9NZ52-4
	GGA3	NM_001172704.3		c.-228+276G>T		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+23C>A		intron	N/A	ENSP00000245539.6	Q9Y2R9
	MRPS7	ENST00000579002.5	TSL:2	c.-321C>A		5_prime_UTR	Exon 1 of 4	ENSP00000463683.1	J3QLS3
	GGA3	ENST00000582717.5	TSL:2	c.-177+276G>T		intron	N/A	ENSP00000462081.1	Q9NZ52-4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000189 AC: 8 AN: 423264 Hom.: 0 Cov.: 0 AF XY: 0.0000192 AC XY: 4 AN XY: 208756

African (AFR) AF: 0.00 AC: 0 AN: 6042

American (AMR) AF: 0.00 AC: 0 AN: 7776

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11770

East Asian (EAS) AF: 0.000237 AC: 1 AN: 4224

South Asian (SAS) AF: 0.00 AC: 0 AN: 14040

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8190

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2586

European-Non Finnish (NFE) AF: 0.0000199 AC: 7 AN: 351240

Other (OTH) AF: 0.00 AC: 0 AN: 17396

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.7
DANN	Benign	0.58
PhyloP100		0.0
PromoterAI		0.0058	Neutral
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		3.5

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: rs62085969; hg19: chr17-73258087;