rs10486771

chr7-15652525-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.518-25607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,132 control chromosomes in the GnomAD database, including 966 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 0.10 (966 hom., cov: 33)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEOX2	NM_005924.5	c.518-25607T>C		intron_variant		ENST00000262041.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEOX2	ENST00000262041.6	c.518-25607T>C		intron_variant		1	NM_005924.5	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15649 AN: 152016 Hom.: 965 Cov.: 33

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.103 AC: 15653 AN: 152132 Hom.: 966 Cov.: 33 AF XY: 0.103 AC XY: 7637 AN XY: 74390

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.131

Alfa AF: 0.123 Hom.: 1584

Bravo AF: 0.106

Asia WGS AF: 0.139 AC: 482 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.71
Dann	Benign	0.76

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: rs10486771; hg19: chr7-15692150;