rs1548691

Positions:

• chr7-15628901-G-A
• chr7-15628901-G-C
• chr7-15628901-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005924.5(MEOX2):​c.518-1983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,918 control chromosomes in the GnomAD database, including 32,934 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 0.66 (32934 hom., cov: 33)
• Consequence: MEOX2 NM_005924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.922

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEOX2	NM_005924.5	c.518-1983C>T		intron_variant		ENST00000262041.6	NP_005915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEOX2	ENST00000262041.6	c.518-1983C>T		intron_variant		1	NM_005924.5	ENSP00000262041	P1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99547 AN: 151800 Hom.: 32902 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.656 AC: 99633 AN: 151918 Hom.: 32934 Cov.: 33 AF XY: 0.653 AC XY: 48460 AN XY: 74238

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.630

Alfa AF: 0.642 Hom.: 47997

Bravo AF: 0.667

Asia WGS AF: 0.604 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1548691; hg19: chr7-15668526;