rs244496

chr12-31057180-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.764+3480G>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 0.922 in 152,140 control chromosomes in the GnomAD database, including 64,712 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 0.92 (64712 hom., cov: 30)
• Consequence: DDX11-AS1 NR_038927.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDX11-AS1	NR_038927.2	n.764+3480G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX11-AS1	ENST00000669174.1	n.592+16015G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140082 AN: 152020 Hom.: 64654 Cov.: 30

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.922 AC: 140200 AN: 152140 Hom.: 64712 Cov.: 30 AF XY: 0.920 AC XY: 68391 AN XY: 74358

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.915

Alfa AF: 0.933 Hom.: 50854

Bravo AF: 0.924

Asia WGS AF: 0.831 AC: 2887 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs244496; hg19: chr12-31210114;