rs7150269

chr14-101568029-A-Cchr14-101568029-A-Gchr14-101568029-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700197.1(DIO3OS):n.622-96T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,066 control chromosomes in the GnomAD database, including 22,232 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 0.53 (22232 hom., cov: 33)
• Consequence: DIO3OS ENST00000700197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIO3OS	ENST00000700197.1	n.622-96T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80772 AN: 151948 Hom.: 22191 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.511

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80879 AN: 152066 Hom.: 22232 Cov.: 33 AF XY: 0.531 AC XY: 39495 AN XY: 74342

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.518

Alfa AF: 0.476 Hom.: 21312

Bravo AF: 0.531

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.48
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7150269; hg19: chr14-102034366;