rs9564840

Positions:

• chr13-71762967-A-G
• chr13-71762967-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080759.6(DACH1):​c.849-81057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,110 control chromosomes in the GnomAD database, including 2,163 homozygotes. 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 0.12 (2163 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

DACH1 (HGNC:2663): (dachshund family transcription factor 1) This gene encodes a chromatin-associated protein that associates with other DNA-binding transcription factors to regulate gene expression and cell fate determination during development. The protein contains a Ski domain that is highly conserved from Drosophila to human. Expression of this gene is lost in some forms of metastatic cancer, and is correlated with poor prognosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DACH1	NM_080759.6	c.849-81057T>C		intron_variant		ENST00000613252.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DACH1	ENST00000613252.5	c.849-81057T>C		intron_variant		1	NM_080759.6	P2
DACH1	ENST00000619232.2	c.849-81057T>C		intron_variant		5		A2
DACH1	ENST00000706274.1	c.392-81057T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17890 AN: 151992 Hom.: 2147 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.118 AC: 17920 AN: 152110 Hom.: 2163 Cov.: 32 AF XY: 0.129 AC XY: 9597 AN XY: 74374

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0912

Gnomad4 OTH AF: 0.134

Alfa AF: 0.119 Hom.: 269

Bravo AF: 0.120

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.39

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: rs9564840; hg19: chr13-72337099;