NM_053281.3:c.1104+1095A>G

Variant names:

• chrX-86715815-A-G
• rs4828153
• NM_053281.3:c.1104+1095A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053281.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DACH2	NM_053281.3	MANE Select	c.1104+1095A>G		intron	N/A	NP_444511.1	Q96NX9-1
	DACH2	NM_001139514.1		c.1065+1095A>G		intron	N/A	NP_001132986.1	A8K3I1
	DACH2	NM_001139515.1		c.603+1095A>G		intron	N/A	NP_001132987.1	Q96NX9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DACH2	ENST00000373125.9	TSL:1 MANE Select	c.1104+1095A>G		intron	N/A	ENSP00000362217.4	Q96NX9-1
	DACH2	ENST00000373131.5	TSL:2	c.1065+1095A>G		intron	N/A	ENSP00000362223.1	Q96NX9-2
	DACH2	ENST00000508860.5	TSL:2	c.603+1095A>G		intron	N/A	ENSP00000420896.1	Q96NX9-4

Frequencies

GnomAD3 genomes AF: 0.849 AC: 93037 AN: 109617 Hom.: 28464 Cov.: 22

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

African (AFR) AF: 0.938 AC: 28304 AN: 30184

American (AMR) AF: 0.873 AC: 8850 AN: 10140

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2024 AN: 2614

East Asian (EAS) AF: 0.655 AC: 2245 AN: 3429

South Asian (SAS) AF: 0.565 AC: 1445 AN: 2558

European-Finnish (FIN) AF: 0.838 AC: 4775 AN: 5701

Middle Eastern (MID) AF: 0.787 AC: 166 AN: 211

European-Non Finnish (NFE) AF: 0.825 AC: 43465 AN: 52655

Other (OTH) AF: 0.848 AC: 1273 AN: 1502

Alfa AF: 0.824 Hom.: 32394

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.56
PhyloP100		0.090
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4828153; hg19: chrX-85970818;