12-65840978-G-A

Variant names:

• chr12-65840978-G-A
• rs12310312
• NM_003483.6:c.249+2409G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003483.6(HMGA2):​c.249+2409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,896 control chromosomes in the GnomAD database, including 7,853 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 0.22 (7853 hom., cov: 32)
• Consequence: HMGA2 NM_003483.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 5 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 5

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• uterine corpus leiomyoma

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003483.6. 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
	HMGA2	NM_003483.6	MANE Select	c.249+2409G>A		intron	N/A	NP_003474.1
	HMGA2	NM_001300919.1		c.249+2409G>A		intron	N/A	NP_001287848.1
	HMGA2	NM_001300918.1		c.249+2409G>A		intron	N/A	NP_001287847.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGA2	ENST00000403681.7	TSL:1 MANE Select	c.249+2409G>A		intron	N/A	ENSP00000384026.2
	HMGA2	ENST00000536545.5	TSL:1	c.249+2409G>A		intron	N/A	ENSP00000437621.1
	HMGA2	ENST00000354636.7	TSL:1	c.249+2409G>A		intron	N/A	ENSP00000346658.3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33494 AN: 151778 Hom.: 7825 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.221 AC: 33580 AN: 151896 Hom.: 7853 Cov.: 32 AF XY: 0.221 AC XY: 16436 AN XY: 74272

African (AFR) AF: 0.588 AC: 24309 AN: 41362

American (AMR) AF: 0.147 AC: 2244 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1214 AN: 5150

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4814

European-Finnish (FIN) AF: 0.0700 AC: 738 AN: 10550

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0468 AC: 3181 AN: 67970

Other (OTH) AF: 0.190 AC: 399 AN: 2104

Alfa AF: 0.141 Hom.: 729

Bravo AF: 0.241

Asia WGS AF: 0.302 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12310312; hg19: chr12-66234758;