rs11148886

Variant names:

• chr13-71706388-G-C
• rs11148886
• NM_080759.6:c.849-24478C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080759.6(DACH1):​c.849-24478C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,870 control chromosomes in the GnomAD database, including 12,061 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 0.25 (12061 hom., cov: 33)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080759.6. 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
	DACH1	NM_080759.6	MANE Select	c.849-24478C>G		intron	N/A	NP_542937.3
	DACH1	NM_001366712.1		c.849-24478C>G		intron	N/A	NP_001353641.1
	DACH1	NM_080760.6		c.849-24478C>G		intron	N/A	NP_542938.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DACH1	ENST00000613252.5	TSL:1 MANE Select	c.849-24478C>G		intron	N/A	ENSP00000482245.1
	DACH1	ENST00000619232.2	TSL:5	c.849-24478C>G		intron	N/A	ENSP00000482797.1
	DACH1	ENST00000706274.1		c.390-24478C>G		intron	N/A	ENSP00000516320.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38485 AN: 151752 Hom.: 12011 Cov.: 33

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.254 AC: 38592 AN: 151870 Hom.: 12061 Cov.: 33 AF XY: 0.249 AC XY: 18463 AN XY: 74224

African (AFR) AF: 0.739 AC: 30627 AN: 41426

American (AMR) AF: 0.148 AC: 2259 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3466

East Asian (EAS) AF: 0.283 AC: 1460 AN: 5158

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4820

European-Finnish (FIN) AF: 0.0189 AC: 199 AN: 10532

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0423 AC: 2872 AN: 67898

Other (OTH) AF: 0.216 AC: 454 AN: 2104

Alfa AF: 0.157 Hom.: 839

Bravo AF: 0.287

Asia WGS AF: 0.223 AC: 770 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.65
PhyloP100		-0.83
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

Other links and lift over

dbSNP: rs11148886; hg19: chr13-72280520;