dbSNP rs11301800: DMXL1:c.4970+14_4970+24delAAAAAAAAAAA (chr5-119165286-TAAAAAAAAAAA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001290321.3(DMXL1):c.4970+14_4970+24delAAAAAAAAAAA variant causes a intron change. The variant allele was found at a frequency of 0.0000124 in 884,614 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

DMXL1
NM_001290321.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.04

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMXL1	NM_001290321.3 link	c.4970+14_4970+24delAAAAAAAAAAA		intron_variant	Intron 21 of 43	ENST00000539542.6	NP_001277250.1	Q9Y485B2RWN7F5H269F1T0K4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMXL1	ENST00000539542.6 link	c.4970+7_4970+17delAAAAAAAAAAA		splice_region_variant, intron_variant	Intron 21 of 43	1	NM_001290321.3	ENSP00000439479.1		F5H269
DMXL1	ENST00000311085.8 link	c.4970+7_4970+17delAAAAAAAAAAA		splice_region_variant, intron_variant	Intron 21 of 42	1		ENSP00000309690.8		Q9Y485

Frequencies

GnomAD3 genomes

AF:

0.0000262

AC:

AN:

114286

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000562

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000104

AC:

AN:

770328

Hom.:

AF XY:

0.0000150

AC XY:

AN XY:

398892

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

17838

American (AMR)

AF:

0.00

AC:

AN:

22268

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16622

East Asian (EAS)

AF:

0.00

AC:

AN:

32276

South Asian (SAS)

AF:

0.00

AC:

AN:

47912

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38062

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2646

European-Non Finnish (NFE)

AF:

0.0000143

AC:

AN:

557914

Other (OTH)

AF:

0.00

AC:

AN:

34790

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.669

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000262

AC:

AN:

114286

Hom.:

Cov.:

AF XY:

0.0000366

AC XY:

AN XY:

54660

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30460

American (AMR)

AF:

0.00

AC:

AN:

11428

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2814

East Asian (EAS)

AF:

0.00

AC:

AN:

4542

South Asian (SAS)

AF:

0.00

AC:

AN:

3622

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5578

Middle Eastern (MID)

AF:

0.00

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.0000562

AC:

AN:

53342

Other (OTH)

AF:

0.00

AC:

AN:

1598

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.0

Splicing

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

Publications

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rs11301800

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over