NM_003483.6:c.249+3115T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003483.6(HMGA2):c.249+3115T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,282 control chromosomes in the GnomAD database, including 476 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.075 ( 476 hom., cov: 32)
Consequence
HMGA2
NM_003483.6 intron
NM_003483.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0110
Publications
8 publications found
Genes affected
HMGA2 (HGNC:5009): (high mobility group AT-hook 2) This gene encodes a protein that belongs to the non-histone chromosomal high mobility group (HMG) protein family. HMG proteins function as architectural factors and are essential components of the enhancesome. This protein contains structural DNA-binding domains and may act as a transcriptional regulating factor. Identification of the deletion, amplification, and rearrangement of this gene that are associated with myxoid liposarcoma suggests a role in adipogenesis and mesenchymal differentiation. A gene knock out study of the mouse counterpart demonstrated that this gene is involved in diet-induced obesity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
HMGA2 Gene-Disease associations (from GenCC):
- Silver-Russell syndrome 5Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- uterine corpus leiomyomaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0746 AC: 11351AN: 152164Hom.: 477 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
11351
AN:
152164
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0745 AC: 11350AN: 152282Hom.: 476 Cov.: 32 AF XY: 0.0759 AC XY: 5654AN XY: 74454 show subpopulations
GnomAD4 genome
AF:
AC:
11350
AN:
152282
Hom.:
Cov.:
32
AF XY:
AC XY:
5654
AN XY:
74454
show subpopulations
African (AFR)
AF:
AC:
2848
AN:
41554
American (AMR)
AF:
AC:
966
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
431
AN:
3470
East Asian (EAS)
AF:
AC:
532
AN:
5182
South Asian (SAS)
AF:
AC:
652
AN:
4820
European-Finnish (FIN)
AF:
AC:
527
AN:
10612
Middle Eastern (MID)
AF:
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5073
AN:
68022
Other (OTH)
AF:
AC:
212
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
557
1113
1670
2226
2783
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
140
280
420
560
700
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
377
AN:
3478
ClinVar
Not reported inComputational 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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