Variant 7-157008772-T-A 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 NM_005515.4(MNX1):c.691+888A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 584,918 control chromosomes in the GnomAD database, including 9,123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 4897 hom., cov: 33)

Exomes 𝑓: 0.12 ( 4226 hom. )

Consequence

MNX1
NM_005515.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.940

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:

MNX1 (HGNC:):

MNX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 7-157008772-T-A is Benign according to our data. Variant chr7-157008772-T-A is described in ClinVar as [Benign]. Clinvar id is 1263676.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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+888A>T		intron_variant		ENST00000252971.11	NP_005506.3	P50219-1
MNX1	NM_001165255.2 linkuse as main transcript	c.55+226A>T		intron_variant			NP_001158727.1	P50219-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MNX1	ENST00000252971.11 linkuse as main transcript	c.691+888A>T		intron_variant		1	NM_005515.4	ENSP00000252971.5		P50219-1

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

31069

AN:

152016

Hom.:

4881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.0975

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.0697

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0989

Gnomad OTH

AF:

0.195

GnomAD3 exomes

AF:

0.159

AC:

8507

AN:

53592

Hom.:

1023

AF XY:

0.156

AC XY:

4220

AN XY:

27056

show subpopulations

Gnomad AFR exome

AF:

0.461

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.0999

Gnomad EAS exome

AF:

0.109

Gnomad SAS exome

AF:

0.203

Gnomad FIN exome

AF:

0.102

Gnomad NFE exome

AF:

0.0950

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.122

AC:

52629

AN:

432784

Hom.:

4226

Cov.:

AF XY:

0.122

AC XY:

27665

AN XY:

226526

show subpopulations

Gnomad4 AFR exome

AF:

0.440

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.182

Gnomad4 FIN exome

AF:

0.0757

Gnomad4 NFE exome

AF:

0.0986

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.205

AC:

31123

AN:

152134

Hom.:

4897

Cov.:

AF XY:

0.203

AC XY:

15089

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.443

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.0975

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.0697

Gnomad4 NFE

AF:

0.0989

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.156

Hom.:

419

Bravo

AF:

0.222

Asia WGS

AF:

0.180

AC:

628

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.3

DANN

Benign

0.91

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