rs1478048014
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_014319.5(LEMD3):c.45G>A(p.Glu15Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000418 in 1,436,708 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: 0.0000042 ( 0 hom. )
Consequence
LEMD3
NM_014319.5 synonymous
NM_014319.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.66
Publications
0 publications found
Genes affected
LEMD3 (HGNC:28887): (LEM domain containing 3) This locus encodes a LEM domain-containing protein. The encoded protein functions to antagonize transforming growth factor-beta signaling at the inner nuclear membrane. Two transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.[provided by RefSeq, Nov 2009]
LEMD3 Gene-Disease associations (from GenCC):
- Buschke-Ollendorff syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
- isolated osteopoikilosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- melorheostosis with osteopoikilosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 12-65169641-G-A is Benign according to our data. Variant chr12-65169641-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1632689.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. GnomAdExome4 allele frequency = 0.00000418 (6/1436708) while in subpopulation AMR AF = 0.000123 (5/40556). AF 95% confidence interval is 0.0000482. There are 0 homozygotes in GnomAdExome4. There are 3 alleles in the male GnomAdExome4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAdExome4 at 6 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014319.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LEMD3 | NM_014319.5 | MANE Select | c.45G>A | p.Glu15Glu | synonymous | Exon 1 of 13 | NP_055134.2 | ||
| LEMD3 | NM_001167614.2 | c.45G>A | p.Glu15Glu | synonymous | Exon 1 of 13 | NP_001161086.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LEMD3 | ENST00000308330.3 | TSL:1 MANE Select | c.45G>A | p.Glu15Glu | synonymous | Exon 1 of 13 | ENSP00000308369.2 | Q9Y2U8 | |
| LEMD3 | ENST00000883212.1 | c.45G>A | p.Glu15Glu | synonymous | Exon 1 of 13 | ENSP00000553271.1 | |||
| LEMD3 | ENST00000935241.1 | c.45G>A | p.Glu15Glu | synonymous | Exon 1 of 13 | ENSP00000605300.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000979 AC: 2AN: 204320 AF XY: 0.0000179 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
204320
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000418 AC: 6AN: 1436708Hom.: 0 Cov.: 32 AF XY: 0.00000421 AC XY: 3AN XY: 712434 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1436708
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
712434
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33192
American (AMR)
AF:
AC:
5
AN:
40556
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25616
East Asian (EAS)
AF:
AC:
0
AN:
38862
South Asian (SAS)
AF:
AC:
0
AN:
82886
European-Finnish (FIN)
AF:
AC:
0
AN:
50362
Middle Eastern (MID)
AF:
AC:
0
AN:
4446
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1101400
Other (OTH)
AF:
AC:
0
AN:
59388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
0
1
2
2
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4
0.00
0.20
0.40
0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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4
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<30
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40-45
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (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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