rs12056299

chr7-15656526-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005924.5(MEOX2):c.517+29360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,246 control chromosomes in the GnomAD database, including 49,751 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 0.81 (49751 hom., cov: 28)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

MEOX2 (HGNC:7014): (mesenchyme homeobox 2) This gene encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes. The encoded protein may play a role in the regulation of vertebrate limb myogenesis. Mutations in the related mouse protein may be associated with craniofacial and/or skeletal abnormalities, in addition to neurovascular dysfunction observed in Alzheimer's disease. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEOX2	NM_005924.5	c.517+29360A>G		intron_variant		ENST00000262041.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEOX2	ENST00000262041.6	c.517+29360A>G		intron_variant		1	NM_005924.5	P1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 121961 AN: 151128 Hom.: 49704 Cov.: 28

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.807 AC: 122060 AN: 151246 Hom.: 49751 Cov.: 28 AF XY: 0.804 AC XY: 59381 AN XY: 73844

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.792

Alfa AF: 0.773 Hom.: 46102

Bravo AF: 0.818

Asia WGS AF: 0.725 AC: 2508 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.73
Dann	Benign	0.51

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

Other links and lift over

dbSNP: rs12056299; hg19: chr7-15696151;