Variant chr7-157008967-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000252971.11(MNX1):c.691+693G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 1,533,750 control chromosomes in the GnomAD database, including 3,275 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.059 ( 264 hom., cov: 33)

Exomes 𝑓: 0.063 ( 3011 hom. )

Consequence

MNX1
ENST00000252971.11 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.114

Variant links:

Genes affected

MNX1 (HGNC:4979): (motor neuron and pancreas homeobox 1) This gene encodes a nuclear protein, which contains a homeobox domain and is a transcription factor. Mutations in this gene result in Currarino syndrome, an autosomic dominant congenital malformation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

MNX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 7-157008967-C-G is Benign according to our data. Variant chr7-157008967-C-G is described in ClinVar as [Benign]. Clinvar id is 1243309.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MNX1	NM_005515.4 linkuse as main transcript	c.691+693G>C		intron_variant		ENST00000252971.11	NP_005506.3
MNX1	NM_001165255.2 linkuse as main transcript	c.55+31G>C		intron_variant			NP_001158727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MNX1	ENST00000252971.11 linkuse as main transcript	c.691+693G>C		intron_variant		1	NM_005515.4	ENSP00000252971	P2	P50219-1

Frequencies

GnomAD3 genomes

AF:

0.0589

AC:

8963

AN:

152206

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0623

Gnomad AMI

AF:

0.0779

Gnomad AMR

AF:

0.0403

Gnomad ASJ

AF:

0.0694

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0341

Gnomad FIN

AF:

0.0495

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0678

Gnomad OTH

AF:

0.0645

GnomAD3 exomes

AF:

0.0494

AC:

7090

AN:

143408

Hom.:

244

AF XY:

0.0500

AC XY:

3830

AN XY:

76648

show subpopulations

Gnomad AFR exome

AF:

0.0607

Gnomad AMR exome

AF:

0.0285

Gnomad ASJ exome

AF:

0.0637

Gnomad EAS exome

AF:

0.000188

Gnomad SAS exome

AF:

0.0368

Gnomad FIN exome

AF:

0.0398

Gnomad NFE exome

AF:

0.0694

Gnomad OTH exome

AF:

0.0525

GnomAD4 exome

AF:

0.0635

AC:

87677

AN:

1381426

Hom.:

3011

Cov.:

AF XY:

0.0624

AC XY:

42572

AN XY:

681838

show subpopulations

Gnomad4 AFR exome

AF:

0.0663

Gnomad4 AMR exome

AF:

0.0290

Gnomad4 ASJ exome

AF:

0.0668

Gnomad4 EAS exome

AF:

0.000140

Gnomad4 SAS exome

AF:

0.0381

Gnomad4 FIN exome

AF:

0.0452

Gnomad4 NFE exome

AF:

0.0691

Gnomad4 OTH exome

AF:

0.0610

GnomAD4 genome

AF:

0.0589

AC:

8965

AN:

152324

Hom.:

264

Cov.:

AF XY:

0.0576

AC XY:

4287

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0621

Gnomad4 AMR

AF:

0.0402

Gnomad4 ASJ

AF:

0.0694

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0348

Gnomad4 FIN

AF:

0.0495

Gnomad4 NFE

AF:

0.0678

Gnomad4 OTH

AF:

0.0639

Alfa

AF:

0.0661

Hom.:

Bravo

AF:

0.0591

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.4

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over