chr7-55955288-T-C

Variant names:

• chr7-55955288-T-C
• rs15892
• NM_015969.3:c.*110T>C

Variant summary

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

The NM_015969.3(MRPS17):​c.*110T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 1,353,814 control chromosomes in the GnomAD database, including 406,474 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 0.82 (51658 hom., cov: 33)
  • Exomes 𝑓: 0.77 (354816 hom.)
• Consequence: MRPS17 NM_015969.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 19 publications found

Genes affected

MRPS17 (HGNC:14047): (mitochondrial ribosomal protein S17) 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 belongs to the ribosomal protein S17P family. The encoded protein is moderately conserved between human mitochondrial and prokaryotic ribosomal proteins. Pseudogenes corresponding to this gene are found on chromosomes 1p, 3p, 6q, 14p, 18q, and Xq. [provided by RefSeq, Jul 2008]

NIPSNAP2 (HGNC:4179): (nipsnap homolog 2) This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. The encoded protein is localized to mitochondria and plays a role in oxidative phosphorylation. A pseudogene of this gene is located on the long arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

ENSG00000249773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015969.3. 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
	MRPS17	NM_015969.3	MANE Select	c.*110T>C		3_prime_UTR	Exon 3 of 3	NP_057053.1	Q9Y2R5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS17	ENST00000285298.9	TSL:1 MANE Select	c.*110T>C		3_prime_UTR	Exon 3 of 3	ENSP00000285298.4	Q9Y2R5
	MRPS17	ENST00000909935.1		c.*110T>C		3_prime_UTR	Exon 3 of 3	ENSP00000579994.1
	MRPS17	ENST00000909936.1		c.*110T>C		3_prime_UTR	Exon 3 of 3	ENSP00000579995.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124683 AN: 152120 Hom.: 51606 Cov.: 33

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.767 AC: 921627 AN: 1201576 Hom.: 354816 Cov.: 17 AF XY: 0.766 AC XY: 453476 AN XY: 592328

African (AFR) AF: 0.953 AC: 25470 AN: 26734

American (AMR) AF: 0.776 AC: 18562 AN: 23932

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 14612 AN: 18750

East Asian (EAS) AF: 0.952 AC: 35267 AN: 37048

South Asian (SAS) AF: 0.750 AC: 47727 AN: 63612

European-Finnish (FIN) AF: 0.782 AC: 37256 AN: 47666

Middle Eastern (MID) AF: 0.751 AC: 3598 AN: 4794

European-Non Finnish (NFE) AF: 0.754 AC: 700220 AN: 928482

Other (OTH) AF: 0.770 AC: 38915 AN: 50558

GnomAD4 genome AF: 0.820 AC: 124791 AN: 152238 Hom.: 51658 Cov.: 33 AF XY: 0.819 AC XY: 60950 AN XY: 74422

African (AFR) AF: 0.947 AC: 39358 AN: 41576

American (AMR) AF: 0.766 AC: 11691 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.939 AC: 4875 AN: 5192

South Asian (SAS) AF: 0.771 AC: 3719 AN: 4826

European-Finnish (FIN) AF: 0.787 AC: 8318 AN: 10574

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51547 AN: 68010

Other (OTH) AF: 0.786 AC: 1661 AN: 2112

Alfa AF: 0.773 Hom.: 59980

Bravo AF: 0.826

Asia WGS AF: 0.827 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		-0.0010
Mutation Taster		=99/1	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: rs15892; hg19: chr7-56022981;