7-15628445-C-G

Variant names:

• chr7-15628445-C-G
• rs6953784
• NM_005924.5:c.518-1527G>C

Variant summary

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

The NM_005924.5(MEOX2):​c.518-1527G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,628 control chromosomes in the GnomAD database, including 32,678 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 0.65 (32678 hom., cov: 33)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	NM_005924.5	MANE Select	c.518-1527G>C		intron	N/A	NP_005915.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	ENST00000262041.6	TSL:1 MANE Select	c.518-1527G>C		intron	N/A	ENSP00000262041.5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99103 AN: 151510 Hom.: 32646 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.654 AC: 99189 AN: 151628 Hom.: 32678 Cov.: 33 AF XY: 0.651 AC XY: 48212 AN XY: 74084

African (AFR) AF: 0.682 AC: 28205 AN: 41352

American (AMR) AF: 0.682 AC: 10380 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3466

East Asian (EAS) AF: 0.804 AC: 4130 AN: 5136

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4812

European-Finnish (FIN) AF: 0.651 AC: 6846 AN: 10518

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.639 AC: 43364 AN: 67822

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

Alfa AF: 0.556 Hom.: 1724

Bravo AF: 0.666

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.031
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: rs6953784; hg19: chr7-15668070;