NM_005924.5:c.518-1152C>A

Variant names:

• chr7-15628070-G-T
• rs7786661
• NM_005924.5:c.518-1152C>A

Variant summary

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

The NM_005924.5(MEOX2):​c.518-1152C>A 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 151,766 control chromosomes in the GnomAD database, including 32,756 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 (32756 hom., cov: 31)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEOX2	NM_005924.5	c.518-1152C>A		intron_variant	Intron 1 of 2	ENST00000262041.6	NP_005915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEOX2	ENST00000262041.6	c.518-1152C>A		intron_variant	Intron 1 of 2	1	NM_005924.5	ENSP00000262041.5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99242 AN: 151648 Hom.: 32724 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.654

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: 0.654 AC: 99327 AN: 151766 Hom.: 32756 Cov.: 31 AF XY: 0.651 AC XY: 48279 AN XY: 74114

African (AFR) AF: 0.680 AC: 28154 AN: 41402

American (AMR) AF: 0.683 AC: 10375 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1913 AN: 3462

East Asian (EAS) AF: 0.809 AC: 4170 AN: 5156

South Asian (SAS) AF: 0.497 AC: 2392 AN: 4814

European-Finnish (FIN) AF: 0.654 AC: 6889 AN: 10540

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

European-Non Finnish (NFE) AF: 0.640 AC: 43460 AN: 67882

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.653 Hom.: 5666

Bravo AF: 0.665

Asia WGS AF: 0.601 AC: 2080 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		0.0080
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: rs7786661; hg19: chr7-15667695;