chr13-71791117-C-T

Variant names:

• chr13-71791117-C-T
• rs9318029
• NM_080759.6:c.848+74805G>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.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
• Publications: 2 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=-0.87).
• 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 rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.848+74805G>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.848+74805G>A		intron_variant	Intron 1 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.848+74805G>A		intron_variant	Intron 1 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.389+74805G>A		intron_variant	Intron 1 of 9			ENSP00000516320.1

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

African (AFR) AF: 0.0994 AC: 4125 AN: 41510

American (AMR) AF: 0.228 AC: 3484 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1089 AN: 3462

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5178

South Asian (SAS) AF: 0.160 AC: 769 AN: 4816

European-Finnish (FIN) AF: 0.313 AC: 3300 AN: 10530

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19755 AN: 67950

Other (OTH) AF: 0.211 AC: 445 AN: 2106

Alfa AF: 0.235 Hom.: 591

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
PhyloP100		-1.3
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: rs9318029; hg19: chr13-72365249;