1-92247304-CAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_053274.3(GLMN):c.1586-162_1586-161del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,892 control chromosomes in the GnomAD database, including 6,481 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (6481 hom., cov: 23)
• Consequence: GLMN NM_053274.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 1-92247304-CAG-C is Benign according to our data. Variant chr1-92247304-CAG-C is described in ClinVar as [Benign]. Clinvar id is 1294738.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLMN	NM_053274.3	c.1586-162_1586-161del		intron_variant		ENST00000370360.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLMN	ENST00000370360.8	c.1586-162_1586-161del		intron_variant		1	NM_053274.3	P1
GLMN	ENST00000495106.5	c.*247-162_*247-161del		intron_variant, NMD_transcript_variant		1
GLMN	ENST00000495852.6	c.809-162_809-161del		intron_variant		5
GLMN	ENST00000471465.1	n.532-162_532-161del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39435 AN: 151776 Hom.: 6472 Cov.: 23

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.260 AC: 39461 AN: 151892 Hom.: 6481 Cov.: 23 AF XY: 0.261 AC XY: 19390 AN XY: 74208

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.266

Alfa AF: 0.309 Hom.: 991

Bravo AF: 0.246

Asia WGS AF: 0.127 AC: 443 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs71586740; hg19: chr1-92712861;