11-119445079-T-C

Variant names:

• chr11-119445079-T-C
• rs4938659
• ENST00000529668.1:n.441A>G

Variant summary

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

The ENST00000529668.1(DUXAP5):​n.441A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,096 control chromosomes in the GnomAD database, including 26,272 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 0.58 (26271 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: DUXAP5 ENST00000529668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 5 publications found

Genes affected

DUXAP5 (HGNC:32184): (double homeobox A pseudogene 5) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This pseudogene is a member of the DUXA homeobox gene family. [provided by RefSeq, Jul 2008]

USP2-AS1 (HGNC:48673): (USP2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529668.1. 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
	USP2-AS1	NR_034160.1		n.306-24730T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUXAP5	ENST00000529668.1	TSL:6	n.441A>G		non_coding_transcript_exon	Exon 1 of 1
	USP2-AS1	ENST00000498979.9	TSL:3	n.327-24730T>C		intron	N/A
	USP2-AS1	ENST00000500970.5	TSL:2	n.273+49925T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88504 AN: 151976 Hom.: 26266 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.602

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 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) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.582 AC: 88551 AN: 152094 Hom.: 26271 Cov.: 32 AF XY: 0.588 AC XY: 43707 AN XY: 74346

African (AFR) AF: 0.491 AC: 20387 AN: 41486

American (AMR) AF: 0.570 AC: 8715 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4473 AN: 5178

South Asian (SAS) AF: 0.790 AC: 3796 AN: 4806

European-Finnish (FIN) AF: 0.584 AC: 6175 AN: 10568

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40882 AN: 67978

Other (OTH) AF: 0.604 AC: 1275 AN: 2110

Alfa AF: 0.583 Hom.: 7580

Bravo AF: 0.575

Asia WGS AF: 0.786 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4938659; hg19: chr11-119315789;