NM_016065.4:c.*633delT

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS16	NM_016065.4	c.*633delT		3_prime_UTR_variant	Exon 3 of 3	ENST00000372945.8	NP_057149.1
MRPS16	XM_047425263.1	c.*633delT		3_prime_UTR_variant	Exon 3 of 3		XP_047281219.1
MRPS16	NM_001410935.1	c.275-901delT		intron_variant	Intron 2 of 2		NP_001397864.1
DNAJC9-AS1	NR_038373.1	n.175+1784delA		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPS16	ENST00000372945	c.*633delT		3_prime_UTR_variant	Exon 3 of 3	1	NM_016065.4	ENSP00000362036.3
DNAJC9-AS1	ENST00000440197.2	n.182+1784delA		intron_variant	Intron 2 of 3	1
MRPS16	ENST00000372940.3	c.275-901delT		intron_variant	Intron 2 of 2	2		ENSP00000362031.3
MRPS16	ENST00000479005.1	n.1204delT		non_coding_transcript_exon_variant	Exon 3 of 3	2

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

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.313

Gnomad4 SAS exome AF: 0.382

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.188

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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0999

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.0707

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs555061429; hg19: chr10-75009976;