rs1190715

chr14-101556742-T-Cchr14-101556742-T-G

Variant summary

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

The NR_152588.1(DIO3OS):n.171+3510A>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 0.574 in 151,974 control chromosomes in the GnomAD database, including 26,425 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 0.57 (26425 hom., cov: 32)
• Consequence: DIO3OS NR_152588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIO3OS	NR_152588.1	n.171+3510A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIO3OS	ENST00000557109.6	n.169+3510A>G		intron_variant, non_coding_transcript_variant		1
DIO3OS	ENST00000700216.1	n.123-1066A>G		intron_variant, non_coding_transcript_variant
DIO3OS	ENST00000700217.1	n.370-1066A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87190 AN: 151856 Hom.: 26370 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.575 AC: 87309 AN: 151974 Hom.: 26425 Cov.: 32 AF XY: 0.570 AC XY: 42319 AN XY: 74266

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.547

Alfa AF: 0.500 Hom.: 15924

Bravo AF: 0.577

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	6.3
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1190715; hg19: chr14-102023079;