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. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_024374.1(LOC642846):​n.241-1163T>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: LOC642846 NR_024374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

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

LOC642846 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -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
SNORA75	ENST00000391138.1	n.-217A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 25467 AN: 95618 Hom.: 927 Cov.: 17 FAILED QC

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

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.260

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4516053; hg19: chr12-9439635;