12-31057743-C-G

Position:

• chr12-31057743-C-G

Variant summary

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

The NR_038927.2(DDX11-AS1):​n.764+2917G>C 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 0.199 in 152,036 control chromosomes in the GnomAD database, including 3,334 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 0.20 (3334 hom., cov: 32)
• Consequence: DDX11-AS1 NR_038927.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDX11-AS1	NR_038927.2	n.764+2917G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX11-AS1	ENST00000669174.1	n.592+15452G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30141 AN: 151918 Hom.: 3320 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.199 AC: 30183 AN: 152036 Hom.: 3334 Cov.: 32 AF XY: 0.201 AC XY: 14941 AN XY: 74332

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0941 Hom.: 136

Bravo AF: 0.208

Asia WGS AF: 0.293 AC: 1015 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7973425; hg19: chr12-31210677;