NM_015084.3:c.282-23358T>C

Variant names:

• chr5-72261486-A-G
• rs17376173
• NM_015084.3:c.282-23358T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015084.3(MRPS27):​c.282-23358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,442 control chromosomes in the GnomAD database, including 5,210 homozygotes. 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: 𝑓 0.23 (5210 hom., cov: 31)
• Consequence: MRPS27 NM_015084.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 1 publications found

Genes affected

MRPS27 (HGNC:14512): (mitochondrial ribosomal protein S27) 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 that may be a functional partner of the death associated protein 3 (DAP3). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015084.3. 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
	MRPS27	NM_015084.3	MANE Select	c.282-23358T>C		intron	N/A	NP_055899.2
	MRPS27	NM_001286748.2		c.282-19798T>C		intron	N/A	NP_001273677.1
	MRPS27	NM_001286751.2		c.114-23358T>C		intron	N/A	NP_001273680.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS27	ENST00000261413.10	TSL:1 MANE Select	c.282-23358T>C		intron	N/A	ENSP00000261413.5
	MRPS27	ENST00000515404.5	TSL:1	n.268-23358T>C		intron	N/A
	MRPS27	ENST00000695404.1		c.282-23358T>C		intron	N/A	ENSP00000511886.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35106 AN: 151324 Hom.: 5209 Cov.: 31

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.217

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.232 AC: 35101 AN: 151442 Hom.: 5210 Cov.: 31 AF XY: 0.232 AC XY: 17169 AN XY: 73996

African (AFR) AF: 0.0688 AC: 2830 AN: 41162

American (AMR) AF: 0.192 AC: 2927 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3464

East Asian (EAS) AF: 0.0238 AC: 123 AN: 5160

South Asian (SAS) AF: 0.280 AC: 1341 AN: 4784

European-Finnish (FIN) AF: 0.344 AC: 3596 AN: 10468

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22668 AN: 67834

Other (OTH) AF: 0.214 AC: 450 AN: 2104

Alfa AF: 0.204 Hom.: 637

Bravo AF: 0.209

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.99
DANN	Benign	0.82
PhyloP100		0.18
Mutation Taster		=100/0	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: rs17376173; hg19: chr5-71557313;