12-31060801-C-T

Position:

• chr12-31060801-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038927.2(DDX11-AS1):​n.654-31G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,012 control chromosomes in the GnomAD database, including 23,098 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 0.54 (23098 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DDX11-AS1 NR_038927.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

DDX11-AS1 (HGNC:44176): (DDX11 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX11-AS1	NR_038927.2	n.654-31G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX11-AS1	ENST00000669174.1	n.592+12394G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81447 AN: 151894 Hom.: 23044 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.517

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.537 AC: 81555 AN: 152012 Hom.: 23098 Cov.: 32 AF XY: 0.539 AC XY: 40039 AN XY: 74296

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.516

Alfa AF: 0.500 Hom.: 3367

Bravo AF: 0.559

Asia WGS AF: 0.691 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4356315; hg19: chr12-31213735;