rs9564840

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080759.6(DACH1):​c.849-81057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,110 control chromosomes in the GnomAD database, including 2,163 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 0.12 ( 2163 hom., cov: 32)

Consequence

DACH1
NM_080759.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DACH1NM_080759.6 linkuse as main transcriptc.849-81057T>C intron_variant ENST00000613252.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DACH1ENST00000613252.5 linkuse as main transcriptc.849-81057T>C intron_variant 1 NM_080759.6 P2Q9UI36-2
DACH1ENST00000619232.2 linkuse as main transcriptc.849-81057T>C intron_variant 5 A2Q9UI36-1
DACH1ENST00000706274.1 linkuse as main transcriptc.392-81057T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.118
AC:
17890
AN:
151992
Hom.:
2147
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0314
Gnomad AMI
AF:
0.0789
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.0773
Gnomad EAS
AF:
0.550
Gnomad SAS
AF:
0.379
Gnomad FIN
AF:
0.118
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0912
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.118
AC:
17920
AN:
152110
Hom.:
2163
Cov.:
32
AF XY:
0.129
AC XY:
9597
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.0314
Gnomad4 AMR
AF:
0.252
Gnomad4 ASJ
AF:
0.0773
Gnomad4 EAS
AF:
0.550
Gnomad4 SAS
AF:
0.381
Gnomad4 FIN
AF:
0.118
Gnomad4 NFE
AF:
0.0912
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.119
Hom.:
269
Bravo
AF:
0.120
Asia WGS
AF:
0.440
AC:
1526
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.3
DANN
Benign
0.39

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9564840; hg19: chr13-72337099; API