rs7150269

Variant names:

• chr14-101568029-A-C
• rs7150269
• ENST00000700197.1:n.622-96T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-101568029-A-C
• chr14-101568029-A-G
• chr14-101568029-A-T

Variant summary

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

The ENST00000700197.1(DIO3OS):​n.622-96T>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 3 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]

LOC105370675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370675	XR_944225.3	n.-185T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIO3OS	ENST00000700197.1	n.622-96T>G		intron_variant	Intron 3 of 8

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

African (AFR) AF: 0.679 AC: 28170 AN: 41468

American (AMR) AF: 0.455 AC: 6957 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2272 AN: 5176

South Asian (SAS) AF: 0.591 AC: 2848 AN: 4822

European-Finnish (FIN) AF: 0.506 AC: 5357 AN: 10586

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.472 AC: 32090 AN: 67944

Other (OTH) AF: 0.518 AC: 1092 AN: 2110

Alfa AF: 0.490 Hom.: 63743

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7150269; hg19: chr14-102034366;