11-64805746-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001370259.2(MEN1):c.1074G>A(p.Glu358Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
MEN1
NM_001370259.2 synonymous
NM_001370259.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.65
Publications
0 publications found
Genes affected
MEN1 (HGNC:7010): (menin 1) This gene encodes menin, a tumor suppressor associated with a syndrome known as multiple endocrine neoplasia type 1. Menin is a scaffold protein that functions in histone modification and epigenetic gene regulation. It is thought to regulate several pathways and processes by altering chromatin structure through the modification of histones. [provided by RefSeq, May 2019]
MEN1 Gene-Disease associations (from GenCC):
- multiple endocrine neoplasia type 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet, Ambry Genetics
- familial isolated hyperparathyroidismInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- pituitary gigantismInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary pheochromocytoma-paragangliomaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
Variant 11-64805746-C-T is Benign according to our data. Variant chr11-64805746-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 412584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.64 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001370259.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MEN1 | NM_001370259.2 | MANE Select | c.1074G>A | p.Glu358Glu | synonymous | Exon 8 of 10 | NP_001357188.2 | ||
| MEN1 | NM_001407150.1 | c.1215G>A | p.Glu405Glu | synonymous | Exon 9 of 11 | NP_001394079.1 | |||
| MEN1 | NM_001370251.2 | c.1200G>A | p.Glu400Glu | synonymous | Exon 9 of 11 | NP_001357180.2 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MEN1 | ENST00000450708.7 | TSL:5 MANE Select | c.1074G>A | p.Glu358Glu | synonymous | Exon 8 of 10 | ENSP00000394933.3 | ||
| MEN1 | ENST00000312049.11 | TSL:1 | c.1074G>A | p.Glu358Glu | synonymous | Exon 8 of 10 | ENSP00000308975.6 | ||
| MEN1 | ENST00000424912.2 | TSL:1 | c.1074G>A | p.Glu358Glu | synonymous | Exon 9 of 11 | ENSP00000388016.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251484 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251484
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727220 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1461828
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
727220
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44718
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86252
European-Finnish (FIN)
AF:
AC:
0
AN:
53412
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1111976
Other (OTH)
AF:
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
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0
1
1
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2
0.00
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0.60
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0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions as Germline
Significance:Benign/Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
2
Multiple endocrine neoplasia, type 1 (2)
-
-
1
Hereditary cancer-predisposing syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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