X-86182773-G-A

Variant names:

• chrX-86182773-G-A
• rs242866
• NM_053281.3:c.488+33665G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_053281.3(DACH2):​c.488+33665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000967 in 103,394 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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 0.0000097 (0 hom., 0 hem., cov: 24)
• Consequence: DACH2 NM_053281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• 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.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DACH2	NM_053281.3	MANE Select	c.488+33665G>A		intron	N/A	NP_444511.1
	DACH2	NM_001139514.1		c.488+33665G>A		intron	N/A	NP_001132986.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DACH2	ENST00000373125.9	TSL:1 MANE Select	c.488+33665G>A		intron	N/A	ENSP00000362217.4
	DACH2	ENST00000373131.5	TSL:2	c.488+33665G>A		intron	N/A	ENSP00000362223.1
	DACH2	ENST00000461604.6	TSL:5	n.488+33665G>A		intron	N/A	ENSP00000421509.1

Frequencies

GnomAD3 genomes AF: 0.00000967 AC: 1 AN: 103394 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000197

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000967 AC: 1 AN: 103394 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 26082

African (AFR) AF: 0.00 AC: 0 AN: 28618

American (AMR) AF: 0.00 AC: 0 AN: 9163

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2517

East Asian (EAS) AF: 0.00 AC: 0 AN: 3237

South Asian (SAS) AF: 0.00 AC: 0 AN: 2060

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4913

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 221

European-Non Finnish (NFE) AF: 0.0000197 AC: 1 AN: 50645

Other (OTH) AF: 0.00 AC: 0 AN: 1366

Alfa AF: 0.00 Hom.: 38

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		0.33

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: rs242866; hg19: chrX-85437777;