rs9318026

chr13-71732113-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DACH1	NM_080759.6	c.849-50203A>G		intron_variant		ENST00000613252.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DACH1	ENST00000613252.5	c.849-50203A>G		intron_variant		1	NM_080759.6	P2
DACH1	ENST00000619232.2	c.849-50203A>G		intron_variant		5		A2
DACH1	ENST00000706274.1	c.392-50203A>G		intron_variant

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

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.647

Alfa AF: 0.820 Hom.: 73037

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318026; hg19: chr13-72306245;