Variant chr5-119165286-T-TAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000539542.6(DMXL1):c.4970+23_4970+24dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00064 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0016 ( 0 hom. )

Consequence

DMXL1
ENST00000539542.6 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.401

Variant links:

Genes affected

DMXL1 (HGNC:2937): (Dmx like 1) The protein encoded by this gene is a member of the WD repeat superfamily of proteins, which have regulatory functions. This gene is expressed in many tissue types including several types of eye tissue, and it has been associated with ocular phenotypes. In addition, it is upregulated in cultured cells that overexpress growth factor independence 1B, a transcription factor that is essential for hematopoietic cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

DMXL1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DMXL1	NM_001290321.3 linkuse as main transcript	c.4970+23_4970+24dup		splice_region_variant, intron_variant		ENST00000539542.6	NP_001277250.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMXL1	ENST00000539542.6 linkuse as main transcript	c.4970+23_4970+24dup		splice_region_variant, intron_variant		1	NM_001290321.3	ENSP00000439479	A1
DMXL1	ENST00000311085.8 linkuse as main transcript	c.4970+23_4970+24dup		splice_region_variant, intron_variant		1		ENSP00000309690	P3

Frequencies

GnomAD3 genomes

AF:

0.000639

AC:

AN:

114280

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000875

Gnomad ASJ

AF:

0.000711

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00847

Gnomad NFE

AF:

0.000487

Gnomad OTH

AF:

0.00125

GnomAD4 exome

AF:

0.00158

AC:

1219

AN:

769622

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

636

AN XY:

398502

show subpopulations

Gnomad4 AFR exome

AF:

0.00157

Gnomad4 AMR exome

AF:

0.00103

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.000186

Gnomad4 SAS exome

AF:

0.00307

Gnomad4 FIN exome

AF:

0.00129

Gnomad4 NFE exome

AF:

0.00160

Gnomad4 OTH exome

AF:

0.00124

GnomAD4 genome

AF:

0.000639

AC:

AN:

114272

Hom.:

Cov.:

AF XY:

0.000567

AC XY:

AN XY:

54674

show subpopulations

Gnomad4 AFR

AF:

0.00121

Gnomad4 AMR

AF:

0.0000874

Gnomad4 ASJ

AF:

0.000711

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000833

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000488

Gnomad4 OTH

AF:

0.00125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over