ENST00000500527.1:n.764+3480G>A

Variant names:

• chr12-31057180-C-T
• rs244496
• ENST00000500527.1:n.764+3480G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500527.1(DDX11-AS1):​n.764+3480G>A variant causes a intron 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 ENST00000500527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DDX11-AS1	NR_038927.2	n.764+3480G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX11-AS1	ENST00000500527.1	n.764+3480G>A		intron_variant	Intron 2 of 2	2
DDX11-AS1	ENST00000535870.1	n.91+3480G>A		intron_variant	Intron 1 of 1	4
DDX11-AS1	ENST00000669174.1	n.592+16015G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.921 AC: 38227 AN: 41512

American (AMR) AF: 0.950 AC: 14526 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3179 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3768 AN: 5150

South Asian (SAS) AF: 0.877 AC: 4209 AN: 4800

European-Finnish (FIN) AF: 0.919 AC: 9721 AN: 10578

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63551 AN: 68012

Other (OTH) AF: 0.915 AC: 1934 AN: 2114

Alfa AF: 0.934 Hom.: 68638

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs244496; hg19: chr12-31210114;