13-71866526-TGCCGCCGCCGCCGCC-T

Variant names:

• chr13-71866526-TGCCGCCGCCGCCGCC-T
• rs748058171
• NM_080759.6:c.229_243delGGCGGCGGCGGCGGC

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_080759.6(DACH1):​c.229_243delGGCGGCGGCGGCGGC​(p.Gly77_Gly81del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000070 (0 hom., cov: 6)
• Consequence: DACH1 NM_080759.6 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• 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: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_080759.6

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.229_243delGGCGGCGGCGGCGGC	p.Gly77_Gly81del	conservative_inframe_deletion	Exon 1 of 11	ENST00000613252.5	NP_542937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DACH1	ENST00000613252.5	c.229_243delGGCGGCGGCGGCGGC	p.Gly77_Gly81del	conservative_inframe_deletion	Exon 1 of 11	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.229_243delGGCGGCGGCGGCGGC	p.Gly77_Gly81del	conservative_inframe_deletion	Exon 1 of 12	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.-231_-217delGGCGGCGGCGGCGGC		upstream_gene_variant				ENSP00000516320.1

Frequencies

GnomAD3 genomes AF: 0.00000697 AC: 1 AN: 143526 Hom.: 0 Cov.: 6

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000211

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000697 AC: 1 AN: 143526 Hom.: 0 Cov.: 6 AF XY: 0.0000143 AC XY: 1 AN XY: 69740

African (AFR) AF: 0.00 AC: 0 AN: 38978

American (AMR) AF: 0.00 AC: 0 AN: 14548

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3388

East Asian (EAS) AF: 0.000211 AC: 1 AN: 4732

South Asian (SAS) AF: 0.00 AC: 0 AN: 4530

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8882

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 302

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 65346

Other (OTH) AF: 0.00 AC: 0 AN: 1940

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3
Mutation Taster		=200/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs748058171; hg19: chr13-72440658;