rs9318029

Positions:

• chr13-71791117-C-T

Variant summary

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

The NM_080759.6(DACH1):​c.848+74805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,022 control chromosomes in the GnomAD database, including 4,427 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 0.22 (4427 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DACH1	NM_080759.6	c.848+74805G>A		intron_variant		ENST00000613252.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DACH1	ENST00000613252.5	c.848+74805G>A		intron_variant		1	NM_080759.6	P2
DACH1	ENST00000619232.2	c.848+74805G>A		intron_variant		5		A2
DACH1	ENST00000706274.1	c.391+74805G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33316 AN: 151904 Hom.: 4428 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.219 AC: 33312 AN: 152022 Hom.: 4427 Cov.: 32 AF XY: 0.219 AC XY: 16289 AN XY: 74290

Gnomad4 AFR AF: 0.0994

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.211

Alfa AF: 0.241 Hom.: 587

Bravo AF: 0.207

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.67

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: rs9318029; hg19: chr13-72365249;