NM_080759.6:c.2083+1177T>C

Variant names:

• chr13-71473964-A-G
• rs9599848
• NM_080759.6:c.2083+1177T>C

Variant summary

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

The NM_080759.6(DACH1):​c.2083+1177T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,030 control chromosomes in the GnomAD database, including 20,034 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 0.46 (20034 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.2083+1177T>C		intron_variant	Intron 10 of 10	ENST00000613252.5	NP_542937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DACH1	ENST00000613252.5	c.2083+1177T>C		intron_variant	Intron 10 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.2239+1177T>C		intron_variant	Intron 11 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.1462+1177T>C		intron_variant	Intron 9 of 9			ENSP00000516320.1
DACH1	ENST00000706275.1	c.1060+1177T>C		intron_variant	Intron 9 of 9			ENSP00000516321.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70044 AN: 151912 Hom.: 20039 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.461 AC: 70036 AN: 152030 Hom.: 20034 Cov.: 32 AF XY: 0.458 AC XY: 34054 AN XY: 74300

African (AFR) AF: 0.135 AC: 5598 AN: 41520

American (AMR) AF: 0.491 AC: 7496 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1219 AN: 5164

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4820

European-Finnish (FIN) AF: 0.644 AC: 6793 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43546 AN: 67922

Other (OTH) AF: 0.474 AC: 1001 AN: 2110

Alfa AF: 0.572 Hom.: 80500

Bravo AF: 0.435

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.52
PhyloP100		0.26
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: rs9599848; hg19: chr13-72048096;