chr1-92247304-CAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.421
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
GLMNNM_053274.3 linkuse as main transcriptc.1586-162_1586-161del intron_variant ENST00000370360.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GLMNENST00000370360.8 linkuse as main transcriptc.1586-162_1586-161del intron_variant 1 NM_053274.3 P1Q92990-1
GLMNENST00000495106.5 linkuse as main transcriptc.*247-162_*247-161del intron_variant, NMD_transcript_variant 1 Q92990-2
GLMNENST00000495852.6 linkuse as main transcriptc.809-162_809-161del intron_variant 5
GLMNENST00000471465.1 linkuse as main transcriptn.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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 12, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71586740; hg19: chr1-92712861; API