NM_005924.5:c.517+26475C>T

Variant names:

• chr7-15659411-G-A
• rs10278557
• NM_005924.5:c.517+26475C>T

Variant summary

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

The NM_005924.5(MEOX2):​c.517+26475C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,954 control chromosomes in the GnomAD database, including 4,817 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 (4817 hom., cov: 31)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005924.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	NM_005924.5	MANE Select	c.517+26475C>T		intron	N/A	NP_005915.2	P50222

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEOX2	ENST00000262041.6	TSL:1 MANE Select	c.517+26475C>T		intron	N/A	ENSP00000262041.5	P50222
	MEOX2	ENST00000904167.1		c.517+26475C>T		intron	N/A	ENSP00000574226.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37001 AN: 151836 Hom.: 4819 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.244 AC: 37008 AN: 151954 Hom.: 4817 Cov.: 31 AF XY: 0.243 AC XY: 18079 AN XY: 74280

African (AFR) AF: 0.157 AC: 6502 AN: 41436

American (AMR) AF: 0.229 AC: 3502 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3464

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5166

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4820

European-Finnish (FIN) AF: 0.317 AC: 3347 AN: 10544

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19482 AN: 67938

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.272 Hom.: 18228

Bravo AF: 0.236

Asia WGS AF: 0.256 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.81
PhyloP100		-0.12
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: rs10278557; hg19: chr7-15699036;