ENST00000717784.1:n.139-36480C>T

Variant names:

• chr12-45127704-C-T
• rs1903937
• ENST00000717784.1:n.139-36480C>T

Variant summary

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

The ENST00000717784.1(DBX2-AS1):​n.139-36480C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,688 control chromosomes in the GnomAD database, including 7,443 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 0.29 (7443 hom., cov: 31)
• Consequence: DBX2-AS1 ENST00000717784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 2 publications found

Genes affected

DBX2-AS1 (HGNC:55479): (DBX2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717784.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBX2-AS1	ENST00000717784.1		n.139-36480C>T		intron	N/A
	DBX2-AS1	ENST00000829188.1		n.257+24531C>T		intron	N/A
	DBX2-AS1	ENST00000829189.1		n.140+24531C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44252 AN: 151570 Hom.: 7446 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.292 AC: 44254 AN: 151688 Hom.: 7443 Cov.: 31 AF XY: 0.299 AC XY: 22164 AN XY: 74110

African (AFR) AF: 0.132 AC: 5467 AN: 41422

American (AMR) AF: 0.244 AC: 3720 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1780 AN: 5160

South Asian (SAS) AF: 0.532 AC: 2557 AN: 4810

European-Finnish (FIN) AF: 0.425 AC: 4421 AN: 10392

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23742 AN: 67886

Other (OTH) AF: 0.318 AC: 669 AN: 2106

Alfa AF: 0.309 Hom.: 1017

Bravo AF: 0.267

Asia WGS AF: 0.374 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1903937; hg19: chr12-45521487;