7-15684128-C-T

Variant names:

• chr7-15684128-C-T
• rs917440
• NM_005924.5:c.517+1758G>A

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+1758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,972 control chromosomes in the GnomAD database, including 11,072 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 0.36 (11072 hom., cov: 32)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 3 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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+1758G>A		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+1758G>A		intron	N/A	ENSP00000262041.5	P50222
	MEOX2	ENST00000904167.1		c.517+1758G>A		intron	N/A	ENSP00000574226.1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53960 AN: 151854 Hom.: 11074 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.355 AC: 53963 AN: 151972 Hom.: 11072 Cov.: 32 AF XY: 0.357 AC XY: 26481 AN XY: 74252

African (AFR) AF: 0.135 AC: 5617 AN: 41492

American (AMR) AF: 0.463 AC: 7066 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2433 AN: 5170

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4315 AN: 10532

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29969 AN: 67914

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.366 Hom.: 2847

Bravo AF: 0.349

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.18
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs917440;

hg19: chr7-15723753;