rs761202

Variant names:

• chrX-86678036-G-A
• rs761202
• NM_053281.3:c.773-16985G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_053281.3(DACH2):​c.773-16985G>A variant causes a intron change. 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 0.83 (27765 hom., 27121 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: DACH2 NM_053281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.61
• Publications: 1 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).

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.773-16985G>A		intron	N/A	NP_444511.1	Q96NX9-1
	DACH2	NM_001139514.1		c.734-16985G>A		intron	N/A	NP_001132986.1	A8K3I1
	DACH2	NM_001139515.1		c.272-16985G>A		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.773-16985G>A		intron	N/A	ENSP00000362217.4	Q96NX9-1
	DACH2	ENST00000373131.5	TSL:2	c.734-16985G>A		intron	N/A	ENSP00000362223.1	Q96NX9-2
	DACH2	ENST00000508860.5	TSL:2	c.272-16985G>A		intron	N/A	ENSP00000420896.1	Q96NX9-4

Frequencies

GnomAD3 genomes AF: 0.834 AC: 92371 AN: 110704 Hom.: 27764 Cov.: 23

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.773

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.845

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: 0.835 AC: 92427 AN: 110755 Hom.: 27765 Cov.: 23 AF XY: 0.823 AC XY: 27121 AN XY: 32971

African (AFR) AF: 0.969 AC: 29635 AN: 30594

American (AMR) AF: 0.861 AC: 8912 AN: 10356

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 1998 AN: 2636

East Asian (EAS) AF: 0.673 AC: 2333 AN: 3466

South Asian (SAS) AF: 0.536 AC: 1412 AN: 2634

European-Finnish (FIN) AF: 0.729 AC: 4254 AN: 5835

Middle Eastern (MID) AF: 0.760 AC: 165 AN: 217

European-Non Finnish (NFE) AF: 0.793 AC: 41926 AN: 52837

Other (OTH) AF: 0.846 AC: 1277 AN: 1510

Alfa AF: 0.807 Hom.: 87559

Bravo AF: 0.853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		3.6
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs761202;

hg19: chrX-85933039;