rs626277

Variant names:

• chr13-71773564-A-C
• rs626277
• NM_080759.6:c.849-91654T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-71773564-A-C
• chr13-71773564-A-G
• chr13-71773564-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080759.6(DACH1):​c.849-91654T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,726 control chromosomes in the GnomAD database, including 21,183 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 0.51 (21183 hom., cov: 33)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 42 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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.849-91654T>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.849-91654T>G		intron_variant	Intron 1 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.849-91654T>G		intron_variant	Intron 1 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.390-91654T>G		intron_variant	Intron 1 of 9			ENSP00000516320.1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77325 AN: 151608 Hom.: 21133 Cov.: 33

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.510 AC: 77434 AN: 151726 Hom.: 21183 Cov.: 33 AF XY: 0.518 AC XY: 38391 AN XY: 74150

African (AFR) AF: 0.656 AC: 27207 AN: 41448

American (AMR) AF: 0.568 AC: 8646 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3464

East Asian (EAS) AF: 0.870 AC: 4474 AN: 5140

South Asian (SAS) AF: 0.606 AC: 2922 AN: 4820

European-Finnish (FIN) AF: 0.416 AC: 4384 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 26988 AN: 67772

Other (OTH) AF: 0.488 AC: 1028 AN: 2108

Alfa AF: 0.441 Hom.: 54802

Bravo AF: 0.525

Asia WGS AF: 0.727 AC: 2519 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		0.59
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: rs626277; hg19: chr13-72347696;