13-71797339-T-A

Position:

• chr13-71797339-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080759.6(DACH1):​c.848+68583A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,808 control chromosomes in the GnomAD database, including 20,269 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 (20269 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DACH1	NM_080759.6	c.848+68583A>T		intron_variant		ENST00000613252.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DACH1	ENST00000613252.5	c.848+68583A>T		intron_variant		1	NM_080759.6	P2
DACH1	ENST00000619232.2	c.848+68583A>T		intron_variant		5		A2
DACH1	ENST00000706274.1	c.391+68583A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76216 AN: 151690 Hom.: 20228 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.503 AC: 76309 AN: 151808 Hom.: 20269 Cov.: 32 AF XY: 0.514 AC XY: 38110 AN XY: 74178

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.491

Alfa AF: 0.432 Hom.: 1820

Bravo AF: 0.510

Asia WGS AF: 0.718 AC: 2492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.18
DANN	Benign	0.72

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: rs303939; hg19: chr13-72371471;