rs7991293

Variant names:

• chr13-71580743-G-A
• rs7991293
• NM_080759.6:c.1127-7731C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-71580743-G-A
• chr13-71580743-G-C

Variant summary

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

The NM_080759.6(DACH1):​c.1127-7731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,998 control chromosomes in the GnomAD database, including 2,807 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 0.13 (2807 hom., cov: 32)
• Consequence: DACH1 NM_080759.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DACH1	NM_080759.6	c.1127-7731C>T		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.1127-7731C>T		intron_variant	Intron 3 of 10	1	NM_080759.6	ENSP00000482245.1
DACH1	ENST00000619232.2	c.1127-7170C>T		intron_variant	Intron 3 of 11	5		ENSP00000482797.1
DACH1	ENST00000706274.1	c.506-7731C>T		intron_variant	Intron 2 of 9			ENSP00000516320.1
DACH1	ENST00000706275.1	c.104-7731C>T		intron_variant	Intron 2 of 9			ENSP00000516321.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19219 AN: 151880 Hom.: 2786 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.127 AC: 19285 AN: 151998 Hom.: 2807 Cov.: 32 AF XY: 0.124 AC XY: 9219 AN XY: 74302

African (AFR) AF: 0.357 AC: 14768 AN: 41390

American (AMR) AF: 0.0928 AC: 1416 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3468

East Asian (EAS) AF: 0.0372 AC: 192 AN: 5162

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4818

European-Finnish (FIN) AF: 0.0138 AC: 146 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0332 AC: 2257 AN: 68002

Other (OTH) AF: 0.112 AC: 237 AN: 2108

Alfa AF: 0.0795 Hom.: 348

Bravo AF: 0.144

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		0.17
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: rs7991293; hg19: chr13-72154875;