7-15628254-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• 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.518-1336A>G		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.518-1336A>G		intron_variant	Intron 1 of 2	1	NM_005924.5	ENSP00000262041.5

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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.630

Alfa AF: 0.647 Hom.: 5204

Bravo AF: 0.666

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.75

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: rs7805746; hg19: chr7-15667879;