chr12-9283172-A-G

Variant names:

• chr12-9283172-A-G
• rs6487748
• ENST00000539757.1:n.58-477A>G

Variant summary

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

The ENST00000539757.1(DDX12B):​n.58-477A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,058 control chromosomes in the GnomAD database, including 19,629 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 0.50 (19629 hom., cov: 34)
• Consequence: DDX12B ENST00000539757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 7 publications found

Genes affected

DDX12B (HGNC:38668): (DEAD/H-box helicase 12B%2C pseudogene [Source:HGNC Symbol%3BAcc:HGNC:38668])

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 = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX12B	ENST00000539757.1	n.58-477A>G		intron_variant	Intron 1 of 28	6

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76631 AN: 151938 Hom.: 19596 Cov.: 34

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.505 AC: 76716 AN: 152058 Hom.: 19629 Cov.: 34 AF XY: 0.512 AC XY: 38047 AN XY: 74332

African (AFR) AF: 0.531 AC: 22020 AN: 41472

American (AMR) AF: 0.512 AC: 7821 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1667 AN: 5188

South Asian (SAS) AF: 0.661 AC: 3188 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5838 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32549 AN: 67956

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.401 Hom.: 1227

Bravo AF: 0.495

Asia WGS AF: 0.490 AC: 1702 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6487748; hg19: chr12-9435768;