12-31060801-C-T

Variant names:

• chr12-31060801-C-T
• rs4356315
• ENST00000500527.1:n.654-31G>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.654-31G>A variant causes a intron 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 ENST00000500527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX11-AS1	NR_038927.2		n.654-31G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX11-AS1	ENST00000500527.1	TSL:2	n.654-31G>A		intron	N/A
	DDX11-AS1	ENST00000618041.2	TSL:2	n.619-31G>A		intron	N/A
	DDX11-AS1	ENST00000669174.1		n.592+12394G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.675 AC: 27962 AN: 41442

American (AMR) AF: 0.596 AC: 9108 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4213 AN: 5156

South Asian (SAS) AF: 0.569 AC: 2737 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4415 AN: 10570

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30170 AN: 67948

Other (OTH) AF: 0.516 AC: 1090 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4356315;

hg19: chr12-31213735;