rs924463

Variant names:

• chr16-59655524-T-C
• rs924463
• ENST00000603858.1:n.-78T>C

Variant summary

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

The ENST00000603858.1(DUXAP11):​n.-78T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,252 control chromosomes in the GnomAD database, including 241 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 0.053 (241 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: DUXAP11 ENST00000603858.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 1 publications found

Genes affected

DUXAP11 (HGNC:51812): (double homeobox A pseudogene 11)

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 (NFE) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUXAP11	ENST00000603858.1	n.-78T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8043 AN: 152126 Hom.: 238 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.00888

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.0684

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

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: 0.125 AC: 1 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0529 AC: 8053 AN: 152244 Hom.: 241 Cov.: 32 AF XY: 0.0517 AC XY: 3845 AN XY: 74436

African (AFR) AF: 0.0461 AC: 1914 AN: 41556

American (AMR) AF: 0.0606 AC: 926 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3466

East Asian (EAS) AF: 0.00890 AC: 46 AN: 5168

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4830

European-Finnish (FIN) AF: 0.0288 AC: 306 AN: 10620

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4200 AN: 68004

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0522 Hom.: 35

Bravo AF: 0.0560

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs924463; hg19: chr16-59689428;