rs924463

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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 (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

Gnomad4 NFE exome AF: 0.125

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

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0912

Gnomad4 EAS AF: 0.00890

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.0681

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924463; hg19: chr16-59689428;