chr10-73250218-CA-C

Variant names:

• chr10-73250218-CA-C
• rs555061429
• NM_016065.4:c.*633delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_016065.4(MRPS16):​c.*633delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 131,984 control chromosomes in the GnomAD database, including 1,112 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1111 hom., cov: 27)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: MRPS16 NM_016065.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 0 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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.*633delT		3_prime_UTR	Exon 3 of 3	NP_057149.1	Q9Y3D3-1
	MRPS16	NM_001410935.1		c.275-901delT		intron	N/A	NP_001397864.1	A6ND22
	DNAJC9-AS1	NR_038373.1		n.175+1784delA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPS16	ENST00000372945.8	TSL:1 MANE Select	c.*633delT		3_prime_UTR	Exon 3 of 3	ENSP00000362036.3	Q9Y3D3-1
	DNAJC9-AS1	ENST00000440197.2	TSL:1	n.182+1784delA		intron	N/A
	MRPS16	ENST00000372940.3	TSL:2	c.275-901delT		intron	N/A	ENSP00000362031.3	A6ND22

Frequencies

GnomAD3 genomes AF: 0.118 AC: 15440 AN: 131362 Hom.: 1107 Cov.: 27

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.0571

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.110

GnomAD4 exome AF: 0.252 AC: 144 AN: 572 Hom.: 1 Cov.: 0 AF XY: 0.253 AC XY: 93 AN XY: 368

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.240 AC: 12 AN: 50

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.313 AC: 5 AN: 16

South Asian (SAS) AF: 0.382 AC: 13 AN: 34

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.242 AC: 110 AN: 454

Other (OTH) AF: 0.188 AC: 3 AN: 16

GnomAD4 genome AF: 0.118 AC: 15480 AN: 131412 Hom.: 1111 Cov.: 27 AF XY: 0.120 AC XY: 7598 AN XY: 63086

African (AFR) AF: 0.182 AC: 6493 AN: 35706

American (AMR) AF: 0.0999 AC: 1298 AN: 12998

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 386 AN: 3186

East Asian (EAS) AF: 0.306 AC: 1392 AN: 4546

South Asian (SAS) AF: 0.229 AC: 925 AN: 4048

European-Finnish (FIN) AF: 0.0707 AC: 512 AN: 7244

Middle Eastern (MID) AF: 0.0586 AC: 15 AN: 256

European-Non Finnish (NFE) AF: 0.0685 AC: 4165 AN: 60802

Other (OTH) AF: 0.114 AC: 204 AN: 1788

Alfa AF: 0.0182 Hom.: 10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.084
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: rs555061429; hg19: chr10-75009976; COSMIC: COSV107395624; COSMIC: COSV107395624;