rs35752451

Variant names:

• chr1-92247041-GAAA-G
• rs35752451
• NM_053274.3:c.1668+18_1668+20delTTT

Your query was ambiguous. Multiple possible variants found:

• chr1-92247041-GAAA-G
• chr1-92247041-GAAA-GA
• chr1-92247041-GAAA-GAA
• chr1-92247041-GAAA-GAAAA

Variant summary

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

The NM_053274.3(GLMN):​c.1668+18_1668+20delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: GLMN NM_053274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLMN	NM_053274.3	c.1668+18_1668+20delTTT		intron_variant	Intron 18 of 18	ENST00000370360.8	NP_444504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLMN	ENST00000370360.8	c.1668+18_1668+20delTTT		intron_variant	Intron 18 of 18	1	NM_053274.3	ENSP00000359385.3
GLMN	ENST00000495106.5	n.*329+18_*329+20delTTT		intron_variant	Intron 17 of 17	1		ENSP00000436829.1
GLMN	ENST00000471465.1	n.614+18_614+20delTTT		intron_variant	Intron 2 of 2	2
GLMN	ENST00000495852.6	c.*18_*20delTTT		downstream_gene_variant		5		ENSP00000469157.2

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs35752451; hg19: chr1-92712598;