rs9318026

Variant names:

• chr13-71732113-T-C
• rs9318026
• NM_080759.6:c.849-50203A>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.849-50203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,092 control chromosomes in the GnomAD database, including 36,955 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 0.62 (36955 hom., cov: 31)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 5 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 = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.849-50203A>G		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.849-50203A>G		intron_variant	Intron 1 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.849-50203A>G		intron_variant	Intron 1 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.390-50203A>G		intron_variant	Intron 1 of 9			ENSP00000516320.1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94928 AN: 151974 Hom.: 36961 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.624 AC: 94910 AN: 152092 Hom.: 36955 Cov.: 31 AF XY: 0.620 AC XY: 46075 AN XY: 74346

African (AFR) AF: 0.178 AC: 7369 AN: 41482

American (AMR) AF: 0.645 AC: 9841 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2819 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5162

South Asian (SAS) AF: 0.545 AC: 2624 AN: 4818

European-Finnish (FIN) AF: 0.872 AC: 9235 AN: 10586

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59452 AN: 67990

Other (OTH) AF: 0.647 AC: 1368 AN: 2116

Alfa AF: 0.794 Hom.: 105030

Bravo AF: 0.588

Asia WGS AF: 0.355 AC: 1238 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	1.6
DANN	Benign	0.34
PhyloP100		-0.21
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: rs9318026; hg19: chr13-72306245;