rs4828153

chrX-86715815-A-GchrX-86715815-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_053281.3(DACH2):c.1104+1095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.85 (28464 hom., 26830 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: DACH2 NM_053281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

DACH2 (HGNC:16814): (dachshund family transcription factor 2) This gene is one of two genes which encode a protein similar to the Drosophila protein dachshund, a transcription factor involved in cell fate determination in the eye, limb and genital disc of the fly. The encoded protein contains two characteristic dachshund domains: an N-terminal domain responsible for DNA binding and a C-terminal domain responsible for protein-protein interactions. This gene is located on the X chromosome and is subject to inactivation by DNA methylation. The encoded protein may be involved in regulation of organogenesis and myogenesis, and may play a role in premature ovarian failure. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd at 28464 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DACH2	NM_053281.3	c.1104+1095A>G		intron_variant		ENST00000373125.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DACH2	ENST00000373125.9	c.1104+1095A>G		intron_variant		1	NM_053281.3	A2

Frequencies

GnomAD3 genomes AF: 0.849 AC: 93037 AN: 109617 Hom.: 28464 Cov.: 22 AF XY: 0.840 AC XY: 26774 AN XY: 31877

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.847

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.849 AC: 93088 AN: 109670 Hom.: 28464 Cov.: 22 AF XY: 0.840 AC XY: 26830 AN XY: 31940

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.848

Alfa AF: 0.810 Hom.: 20030

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.69
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs4828153; hg19: chrX-85970818;