rs4516053

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-9287039-T-C
• chr12-9287039-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000539757.1(DDX12B):​n.184-1163T>C 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 0.27 (935 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: DDX12B ENST00000539757.1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC642846	NR_024374.1	n.241-1163T>C		intron_variant	Intron 1 of 21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX12B	ENST00000539757.1	n.184-1163T>C		intron_variant	Intron 2 of 28	6
ENSG00000295087	ENST00000727879.1	n.255-1163T>C		intron_variant	Intron 1 of 7
ENSG00000295087	ENST00000727880.1	n.174-1163T>C		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.266 AC: 25467 AN: 95618 Hom.: 927 Cov.: 17

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.263

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.266 AC: 25498 AN: 95684 Hom.: 935 Cov.: 17 AF XY: 0.265 AC XY: 12086 AN XY: 45648

African (AFR) AF: 0.265 AC: 6278 AN: 23702

American (AMR) AF: 0.276 AC: 2703 AN: 9792

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 735 AN: 2194

East Asian (EAS) AF: 0.180 AC: 692 AN: 3848

South Asian (SAS) AF: 0.333 AC: 826 AN: 2484

European-Finnish (FIN) AF: 0.307 AC: 1948 AN: 6352

Middle Eastern (MID) AF: 0.300 AC: 66 AN: 220

European-Non Finnish (NFE) AF: 0.259 AC: 11705 AN: 45108

Other (OTH) AF: 0.260 AC: 350 AN: 1346

Alfa AF: 0.191 Hom.: 120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.27
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;