chr13-71771373-C-T

Variant names:

• chr13-71771373-C-T
• rs584480
• NM_080759.6:c.849-89463G>A

Variant summary

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

The NM_080759.6(DACH1):​c.849-89463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 150,446 control chromosomes in the GnomAD database, including 20,467 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 0.50 (20467 hom., cov: 30)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.849-89463G>A		intron_variant	Intron 1 of 10	ENST00000613252.5	NP_542937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DACH1	ENST00000613252.5	c.849-89463G>A		intron_variant	Intron 1 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.849-89463G>A		intron_variant	Intron 1 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.390-89463G>A		intron_variant	Intron 1 of 9			ENSP00000516320.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 75738 AN: 150328 Hom.: 20417 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.504 AC: 75851 AN: 150446 Hom.: 20467 Cov.: 30 AF XY: 0.511 AC XY: 37575 AN XY: 73532

African (AFR) AF: 0.646 AC: 26646 AN: 41232

American (AMR) AF: 0.564 AC: 8514 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1356 AN: 3456

East Asian (EAS) AF: 0.868 AC: 4479 AN: 5158

South Asian (SAS) AF: 0.578 AC: 2781 AN: 4810

European-Finnish (FIN) AF: 0.415 AC: 4269 AN: 10294

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26381 AN: 67090

Other (OTH) AF: 0.484 AC: 1013 AN: 2094

Alfa AF: 0.449 Hom.: 20233

Bravo AF: 0.518

Asia WGS AF: 0.712 AC: 2460 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		0.18
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: rs584480; hg19: chr13-72345505;