5-119165286-TAAAAAAAAAAA-TAAAA

Variant names:

• chr5-119165286-TAAAAAAA-T
• NM_001290321.3:c.4970+18_4970+24delAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000539542.6(DMXL1):​c.4970+7_4970+13delAAAAAAA variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000974 in 770,146 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000097 (0 hom.)
• Consequence: DMXL1 ENST00000539542.6 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.04

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMXL1	NM_001290321.3	c.4970+18_4970+24delAAAAAAA		intron_variant	Intron 21 of 43	ENST00000539542.6	NP_001277250.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMXL1	ENST00000539542.6	c.4970+7_4970+13delAAAAAAA		splice_region_variant, intron_variant	Intron 21 of 43	1	NM_001290321.3	ENSP00000439479.1
DMXL1	ENST00000311085.8	c.4970+7_4970+13delAAAAAAA		splice_region_variant, intron_variant	Intron 21 of 42	1		ENSP00000309690.8

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000974 AC: 75 AN: 770146 Hom.: 0 AF XY: 0.0000752 AC XY: 30 AN XY: 398784

Gnomad4 AFR exome AF: 0.000112

Gnomad4 AMR exome AF: 0.000270

Gnomad4 ASJ exome AF: 0.000120

Gnomad4 EAS exome AF: 0.0000620

Gnomad4 SAS exome AF: 0.000230

Gnomad4 FIN exome AF: 0.0000789

Gnomad4 NFE exome AF: 0.0000807

Gnomad4 OTH exome AF: 0.000115

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-118500981;