rs6953784

chr7-15628445-C-Gchr7-15628445-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEOX2	NM_005924.5	c.518-1527G>C		intron_variant		ENST00000262041.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEOX2	ENST00000262041.6	c.518-1527G>C		intron_variant		1	NM_005924.5	P1

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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.630

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.4
Dann	Benign	0.34

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: rs6953784; hg19: chr7-15668070;