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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001290321.3(DMXL1):c.4970+24del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 3934 hom., cov: 0)

Exomes 𝑓: 0.26 ( 464 hom. )

Consequence

DMXL1
NM_001290321.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 Benign. Variant got -10 ACMG points.

BP6

Variant 5-119165286-TA-T is Benign according to our data. Variant chr5-119165286-TA-T is described in ClinVar as [Benign]. Clinvar id is 402595.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

32513

AN:

114172

Hom.:

3934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.512

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.280

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.270

GnomAD3 exomes

AF:

0.238

AC:

20661

AN:

86686

Hom.:

AF XY:

0.232

AC XY:

11018

AN XY:

47508

show subpopulations

Gnomad AFR exome

AF:

0.256

Gnomad AMR exome

AF:

0.206

Gnomad ASJ exome

AF:

0.232

Gnomad EAS exome

AF:

0.242

Gnomad SAS exome

AF:

0.187

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.248

GnomAD4 exome

AF:

0.257

AC:

196559

AN:

764058

Hom.:

464

Cov.:

AF XY:

0.254

AC XY:

100500

AN XY:

395466

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.242

Gnomad4 EAS exome

AF:

0.326

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.285

AC:

32514

AN:

114164

Hom.:

3934

Cov.:

AF XY:

0.286

AC XY:

15620

AN XY:

54634

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.511

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.268

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over