13-71600221-C-T

Variant names:

• chr13-71600221-C-T
• rs9919839
• NM_080759.6:c.1127-27209G>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.1127-27209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,108 control chromosomes in the GnomAD database, including 1,537 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 0.11 (1537 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.1127-27209G>A		intron_variant	Intron 3 of 10	ENST00000613252.5	NP_542937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DACH1	ENST00000613252.5	c.1127-27209G>A		intron_variant	Intron 3 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.1127-26648G>A		intron_variant	Intron 3 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.506-27209G>A		intron_variant	Intron 2 of 9			ENSP00000516320.1
DACH1	ENST00000706275.1	c.104-27209G>A		intron_variant	Intron 2 of 9			ENSP00000516321.1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16008 AN: 151990 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.105 AC: 16028 AN: 152108 Hom.: 1537 Cov.: 32 AF XY: 0.115 AC XY: 8535 AN XY: 74352

African (AFR) AF: 0.0457 AC: 1899 AN: 41558

American (AMR) AF: 0.169 AC: 2576 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0966 AC: 335 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2169 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1922 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1191 AN: 10584

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0827 AC: 5617 AN: 67938

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.0933 Hom.: 1572

Bravo AF: 0.105

Asia WGS AF: 0.379 AC: 1317 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.53
DANN	Benign	0.46
PhyloP100		-0.90
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: rs9919839; hg19: chr13-72174353;