rs761202

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH2	NM_053281.3	c.773-16985G>A		intron_variant	Intron 4 of 11	ENST00000373125.9	NP_444511.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DACH2	ENST00000373125.9	c.773-16985G>A		intron_variant	Intron 4 of 11	1	NM_053281.3	ENSP00000362217.4

Frequencies

GnomAD3 genomes AF: 0.834 AC: 92371 AN: 110704 Hom.: 27764 Cov.: 23 AF XY: 0.822 AC XY: 27062 AN XY: 32910

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

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.846

Alfa AF: 0.792 Hom.: 59014

Bravo AF: 0.853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs761202; hg19: chrX-85933039;