rs1190716

Variant names:

• chr14-101558887-C-T
• rs1190716
• ENST00000553575.3:n.106+1365G>A

Variant summary

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

The ENST00000700222.1(DIO3OS):​n.1468G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 213,384 control chromosomes in the GnomAD database, including 2,612 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 0.15 (2229 hom., cov: 32)
  • Exomes 𝑓: 0.091 (383 hom.)
• Consequence: DIO3OS ENST00000700222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 publications found

Genes affected

DIO3OS (HGNC:20348): (DIO3 opposite strand upstream RNA) The mouse and human DIO3OS and DIO3 (MIM 601038) genes overlap and are transcribed in opposite directions. The mouse Dio3 gene is imprinted from the paternal allele during fetal development, suggesting that DIO3OS is a noncoding gene that may have a role in maintaining monoallelic expression of DIO3 (Hernandez et al., 2004 [PubMed 14962667]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700222.1. 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
	DIO3OS	NR_152588.1		n.171+1365G>A		intron	N/A
	DIO3OS	NR_152589.1		n.172-53G>A		intron	N/A
	DIO3OS	NR_152590.1		n.172-53G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIO3OS	ENST00000553575.3	TSL:1	n.106+1365G>A		intron	N/A
	DIO3OS	ENST00000554441.8	TSL:1	n.467-53G>A		intron	N/A
	DIO3OS	ENST00000554694.3	TSL:1	n.232-53G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22534 AN: 149474 Hom.: 2223 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0465

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.00692

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0911 AC: 5809 AN: 63792 Hom.: 383 Cov.: 0 AF XY: 0.0893 AC XY: 2947 AN XY: 32994

African (AFR) AF: 0.249 AC: 563 AN: 2264

American (AMR) AF: 0.0788 AC: 329 AN: 4174

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 109 AN: 1526

East Asian (EAS) AF: 0.00563 AC: 21 AN: 3732

South Asian (SAS) AF: 0.0907 AC: 629 AN: 6936

European-Finnish (FIN) AF: 0.0626 AC: 151 AN: 2412

Middle Eastern (MID) AF: 0.120 AC: 32 AN: 266

European-Non Finnish (NFE) AF: 0.0935 AC: 3643 AN: 38972

Other (OTH) AF: 0.0946 AC: 332 AN: 3510

GnomAD4 genome AF: 0.151 AC: 22580 AN: 149592 Hom.: 2229 Cov.: 32 AF XY: 0.146 AC XY: 10616 AN XY: 72924

African (AFR) AF: 0.289 AC: 11653 AN: 40254

American (AMR) AF: 0.114 AC: 1710 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 296 AN: 3460

East Asian (EAS) AF: 0.00713 AC: 36 AN: 5048

South Asian (SAS) AF: 0.108 AC: 503 AN: 4648

European-Finnish (FIN) AF: 0.0716 AC: 742 AN: 10368

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7294 AN: 67574

Other (OTH) AF: 0.128 AC: 267 AN: 2090

Alfa AF: 0.117 Hom.: 1689

Bravo AF: 0.157

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1190716; hg19: chr14-102025224;