rs548755417

chr7-157009949-AGCGGCGGCGGCGGCG-Achr7-157009949-AGCGGCGGCGGCGGCG-AGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGchr7-157009949-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3

The NM_005515.4(MNX1):c.387_401del(p.Ala130_Ala134del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 908,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000077 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000064 (0 hom.)
• Consequence: MNX1 NM_005515.4 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.14

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]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_005515.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MNX1	NM_005515.4	c.387_401del	p.Ala130_Ala134del	inframe_deletion	1/3	ENST00000252971.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MNX1	ENST00000252971.11	c.387_401del	p.Ala130_Ala134del	inframe_deletion	1/3	1	NM_005515.4	P2

Frequencies

GnomAD3 genomes AF: 0.00000771 AC: 1 AN: 129766 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000285

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000642 AC: 5 AN: 778488 Hom.: 0 AF XY: 0.00000550 AC XY: 2 AN XY: 363726

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000618

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000565

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000771 AC: 1 AN: 129766 Hom.: 0 Cov.: 0 AF XY: 0.0000159 AC XY: 1 AN XY: 62912

Gnomad4 AFR AF: 0.0000285

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs548755417; hg19: chr7-156802643;