rs17336581

Variant names:

• chr7-15652468-A-G
• rs17336581
• NM_005924.5:c.518-25550T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-15652468-A-G
• chr7-15652468-A-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.518-25550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,968 control chromosomes in the GnomAD database, including 5,387 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 (5387 hom., cov: 32)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 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.518-25550T>C		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.518-25550T>C		intron	N/A	ENSP00000262041.5	P50222
	MEOX2	ENST00000904167.1		c.518-25550T>C		intron	N/A	ENSP00000574226.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36340 AN: 151850 Hom.: 5389 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.239 AC: 36335 AN: 151968 Hom.: 5387 Cov.: 32 AF XY: 0.235 AC XY: 17429 AN XY: 74284

African (AFR) AF: 0.0624 AC: 2593 AN: 41552

American (AMR) AF: 0.255 AC: 3889 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3460

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5170

South Asian (SAS) AF: 0.194 AC: 935 AN: 4814

European-Finnish (FIN) AF: 0.275 AC: 2908 AN: 10576

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22603 AN: 67842

Other (OTH) AF: 0.256 AC: 541 AN: 2110

Alfa AF: 0.309 Hom.: 8823

Bravo AF: 0.234

Asia WGS AF: 0.250 AC: 864 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.48
PhyloP100		0.47
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: rs17336581; hg19: chr7-15692093;