7-15628254-T-C

Variant names:

• chr7-15628254-T-C
• rs7805746
• NM_005924.5:c.518-1336A>G

Variant summary

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

The NM_005924.5(MEOX2):​c.518-1336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,832 control chromosomes in the GnomAD database, including 32,861 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 0.66 (32861 hom., cov: 31)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005924.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	NM_005924.5	MANE Select	c.518-1336A>G		intron	N/A	NP_005915.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	ENST00000262041.6	TSL:1 MANE Select	c.518-1336A>G		intron	N/A	ENSP00000262041.5
	MEOX2	ENST00000904167.1		c.518-1336A>G		intron	N/A	ENSP00000574226.1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99394 AN: 151716 Hom.: 32829 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.655 AC: 99480 AN: 151832 Hom.: 32861 Cov.: 31 AF XY: 0.652 AC XY: 48383 AN XY: 74212

African (AFR) AF: 0.683 AC: 28272 AN: 41408

American (AMR) AF: 0.683 AC: 10390 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1915 AN: 3466

East Asian (EAS) AF: 0.808 AC: 4169 AN: 5158

South Asian (SAS) AF: 0.497 AC: 2391 AN: 4812

European-Finnish (FIN) AF: 0.652 AC: 6891 AN: 10564

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43479 AN: 67892

Other (OTH) AF: 0.630 AC: 1328 AN: 2108

Alfa AF: 0.649 Hom.: 5403

Bravo AF: 0.666

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.75
PhyloP100		0.72
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: rs7805746; hg19: chr7-15667879;