1-92247304-CAG-CAGAG

Variant names:

• chr1-92247304-C-CAG
• rs71586740
• NM_053274.3:c.1586-162_1586-161dupCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_053274.3(GLMN):​c.1586-162_1586-161dupCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 23)
• Consequence: GLMN NM_053274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

Genes affected

GLMN (HGNC:14373): (glomulin, FKBP associated protein) This gene encodes a phosphorylated protein that is a member of a Skp1-Cullin-F-box-like complex. The protein is essential for normal development of the vasculature and mutations in this gene have been associated with glomuvenous malformations, also called glomangiomas. Multiple splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLMN	NM_053274.3	c.1586-162_1586-161dupCT		intron_variant	Intron 17 of 18	ENST00000370360.8	NP_444504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLMN	ENST00000370360.8	c.1586-161_1586-160insCT		intron_variant	Intron 17 of 18	1	NM_053274.3	ENSP00000359385.3
GLMN	ENST00000495106.5	n.*247-161_*247-160insCT		intron_variant	Intron 16 of 17	1		ENSP00000436829.1
GLMN	ENST00000495852.6	c.809-161_809-160insCT		intron_variant	Intron 9 of 9	5		ENSP00000469157.2
GLMN	ENST00000471465.1	n.532-161_532-160insCT		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71586740; hg19: chr1-92712861;