12-9287039-T-G

Variant names:

• chr12-9287039-T-G
• rs4516053
• ENST00000539757.1:n.184-1163T>G

Variant summary

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

The NR_024374.1(LOC642846):​n.241-1163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.086 (446 hom., cov: 17)
• Consequence: LOC642846 NR_024374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 1 publications found

Genes affected

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

ENSG00000295087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_024374.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC642846	NR_024374.1		n.241-1163T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX12B	ENST00000539757.1	TSL:6	n.184-1163T>G		intron	N/A
	ENSG00000295087	ENST00000727879.1		n.255-1163T>G		intron	N/A
	ENSG00000295087	ENST00000727880.1		n.174-1163T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 9475 AN: 110676 Hom.: 446 Cov.: 17

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.0407

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0856 AC: 9475 AN: 110754 Hom.: 446 Cov.: 17 AF XY: 0.0835 AC XY: 4388 AN XY: 52576

African (AFR) AF: 0.0477 AC: 1294 AN: 27142

American (AMR) AF: 0.101 AC: 1122 AN: 11154

Ashkenazi Jewish (ASJ) AF: 0.0410 AC: 109 AN: 2660

East Asian (EAS) AF: 0.0157 AC: 68 AN: 4336

South Asian (SAS) AF: 0.0819 AC: 229 AN: 2796

European-Finnish (FIN) AF: 0.0999 AC: 723 AN: 7236

Middle Eastern (MID) AF: 0.0440 AC: 11 AN: 250

European-Non Finnish (NFE) AF: 0.108 AC: 5711 AN: 52840

Other (OTH) AF: 0.0813 AC: 127 AN: 1562

Alfa AF: 0.0589 Hom.: 120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.25
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4516053; hg19: chr12-9439635;