12-31057743-C-G

Variant names:

• chr12-31057743-C-G
• rs7973425
• ENST00000500527.1:n.764+2917G>C

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+2917G>C variant causes a intron 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 ENST00000500527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX11-AS1	NR_038927.2		n.764+2917G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDX11-AS1	ENST00000500527.1	TSL:2	n.764+2917G>C		intron	N/A
	DDX11-AS1	ENST00000535870.1	TSL:4	n.91+2917G>C		intron	N/A
	DDX11-AS1	ENST00000669174.1		n.592+15452G>C		intron	N/A

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

African (AFR) AF: 0.170 AC: 7048 AN: 41462

American (AMR) AF: 0.293 AC: 4481 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2070 AN: 5144

South Asian (SAS) AF: 0.200 AC: 964 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1912 AN: 10580

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12632 AN: 67984

Other (OTH) AF: 0.181 AC: 382 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs7973425; hg19: chr12-31210677;