rs2018198

Variant names:

• chr10-73249349-T-A
• rs2018198
• NM_016065.4:c.*1503A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-73249349-T-A
• chr10-73249349-T-C
• chr10-73249349-T-G

Variant summary

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

The NM_016065.4(MRPS16):​c.*1503A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 1,541,096 control chromosomes in the GnomAD database, including 7,092 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.092 (923 hom., cov: 32)
  • Exomes 𝑓: 0.077 (6169 hom.)
• Consequence: MRPS16 NM_016065.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 17 publications found

Genes affected

MRPS16 (HGNC:14048): (mitochondrial ribosomal protein S16) 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 S16P family. The encoded protein is one of the most highly conserved ribosomal proteins between mammalian and yeast mitochondria. Three pseudogenes (located at 8q21.3, 20q13.32, 22q12-q13.1) for this gene have been described. [provided by RefSeq, Jul 2008]

DNAJC9-AS1 (HGNC:31432): (DNAJC9 and MRPS16 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016065.4. 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
	MRPS16	NM_016065.4	MANE Select	c.*1503A>T		3_prime_UTR	Exon 3 of 3	NP_057149.1	Q9Y3D3-1
	MRPS16	NM_001410935.1		c.275-31A>T		intron	N/A	NP_001397864.1	A6ND22
	DNAJC9-AS1	NR_038373.1		n.175+899T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS16	ENST00000372945.8	TSL:1 MANE Select	c.*1503A>T		3_prime_UTR	Exon 3 of 3	ENSP00000362036.3	Q9Y3D3-1
	DNAJC9-AS1	ENST00000440197.2	TSL:1	n.182+899T>A		intron	N/A
	MRPS16	ENST00000372940.3	TSL:2	c.275-31A>T		intron	N/A	ENSP00000362031.3	A6ND22

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13947 AN: 152062 Hom.: 907 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0973

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0823

GnomAD2 exomes AF: 0.108 AC: 16280 AN: 151346 AF XY: 0.114

Gnomad AFR exome AF: 0.124

Gnomad AMR exome AF: 0.0810

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.297

Gnomad FIN exome AF: 0.0439

Gnomad NFE exome AF: 0.0605

Gnomad OTH exome AF: 0.0872

GnomAD4 exome AF: 0.0773 AC: 107393 AN: 1388916 Hom.: 6169 Cov.: 27 AF XY: 0.0812 AC XY: 55700 AN XY: 685544

African (AFR) AF: 0.118 AC: 3685 AN: 31342

American (AMR) AF: 0.0816 AC: 2899 AN: 35546

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 2490 AN: 25098

East Asian (EAS) AF: 0.284 AC: 10109 AN: 35616

South Asian (SAS) AF: 0.214 AC: 16848 AN: 78806

European-Finnish (FIN) AF: 0.0454 AC: 2184 AN: 48152

Middle Eastern (MID) AF: 0.0574 AC: 318 AN: 5544

European-Non Finnish (NFE) AF: 0.0595 AC: 63773 AN: 1071130

Other (OTH) AF: 0.0882 AC: 5087 AN: 57682

GnomAD4 genome AF: 0.0921 AC: 14010 AN: 152180 Hom.: 923 Cov.: 32 AF XY: 0.0941 AC XY: 7007 AN XY: 74428

African (AFR) AF: 0.121 AC: 5033 AN: 41478

American (AMR) AF: 0.0803 AC: 1229 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0973 AC: 337 AN: 3464

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5180

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4824

European-Finnish (FIN) AF: 0.0416 AC: 442 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4060 AN: 68006

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0472 Hom.: 53

Bravo AF: 0.0936

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2018198; hg19: chr10-75009107;