chr7-15652525-A-G

Variant names:

• chr7-15652525-A-G
• rs10486771
• NM_005924.5:c.518-25607T>C

Variant summary

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

The NM_005924.5(MEOX2):​c.518-25607T>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
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
MEOX2	NM_005924.5	c.518-25607T>C		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.518-25607T>C		intron_variant	Intron 1 of 2	1	NM_005924.5	ENSP00000262041.5

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

African (AFR) AF: 0.0514 AC: 2137 AN: 41562

American (AMR) AF: 0.148 AC: 2255 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3464

East Asian (EAS) AF: 0.154 AC: 796 AN: 5180

South Asian (SAS) AF: 0.163 AC: 788 AN: 4824

European-Finnish (FIN) AF: 0.0911 AC: 967 AN: 10616

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7819 AN: 67924

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.122 Hom.: 1942

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
PhyloP100		-0.73
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: rs10486771; hg19: chr7-15692150;