chr7-15652468-A-G

Position:

• chr7-15652468-A-G

Variant summary

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

The NM_005924.5(MEOX2):​c.518-25550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,968 control chromosomes in the GnomAD database, including 5,387 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 0.24 (5387 hom., cov: 32)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEOX2	NM_005924.5	c.518-25550T>C		intron_variant		ENST00000262041.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEOX2	ENST00000262041.6	c.518-25550T>C		intron_variant		1	NM_005924.5	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36340 AN: 151850 Hom.: 5389 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.239 AC: 36335 AN: 151968 Hom.: 5387 Cov.: 32 AF XY: 0.235 AC XY: 17429 AN XY: 74284

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.256

Alfa AF: 0.310 Hom.: 7328

Bravo AF: 0.234

Asia WGS AF: 0.250 AC: 864 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.48

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: rs17336581; hg19: chr7-15692093;