rs8011440

Positions:

• chr14-101558821-C-T

Variant summary

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

The ENST00000554441.7(DIO3OS):​n.452G>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 0.411 in 242,610 control chromosomes in the GnomAD database, including 20,981 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 0.42 (13208 hom., cov: 31)
  • Exomes 𝑓: 0.40 (7773 hom.)
• Consequence: DIO3OS ENST00000554441.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

Genes affected

DIO3OS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIO3OS	NR_152589.1	n.185G>A		non_coding_transcript_exon_variant	2/4
DIO3OS	NR_152590.1	n.185G>A		non_coding_transcript_exon_variant	2/2
DIO3OS	NR_152591.1	n.185G>A		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIO3OS	ENST00000554441.7	n.452G>A		non_coding_transcript_exon_variant	3/4	1
DIO3OS	ENST00000554694.3	n.245G>A		non_coding_transcript_exon_variant	2/3	1
DIO3OS	ENST00000555174.6	n.191G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63054 AN: 151468 Hom.: 13192 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.402 AC: 36622 AN: 91024 Hom.: 7773 Cov.: 0 AF XY: 0.407 AC XY: 19223 AN XY: 47252

Gnomad4 AFR exome AF: 0.409

Gnomad4 AMR exome AF: 0.415

Gnomad4 ASJ exome AF: 0.323

Gnomad4 EAS exome AF: 0.506

Gnomad4 SAS exome AF: 0.448

Gnomad4 FIN exome AF: 0.394

Gnomad4 NFE exome AF: 0.385

Gnomad4 OTH exome AF: 0.397

GnomAD4 genome AF: 0.416 AC: 63118 AN: 151586 Hom.: 13208 Cov.: 31 AF XY: 0.418 AC XY: 30965 AN XY: 74070

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.426

Alfa AF: 0.411 Hom.: 5229

Bravo AF: 0.413

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8011440; hg19: chr14-102025158;