NM_003483.6:c.249+24046G>C

Variant names:

• chr12-65862615-G-C
• rs11175944
• NM_003483.6:c.249+24046G>C

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+24046G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,132 control chromosomes in the GnomAD database, including 10,884 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 0.27 (10884 hom., cov: 33)
• Consequence: HMGA2 NM_003483.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 10 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-AS1 (HGNC:53973): (HMGA2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGA2	NM_003483.6	MANE Select	c.249+24046G>C		intron	N/A	NP_003474.1
	HMGA2	NM_001300919.1		c.249+24046G>C		intron	N/A	NP_001287848.1
	HMGA2	NM_001300918.1		c.249+24046G>C		intron	N/A	NP_001287847.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGA2	ENST00000403681.7	TSL:1 MANE Select	c.249+24046G>C		intron	N/A	ENSP00000384026.2
	HMGA2	ENST00000536545.5	TSL:1	c.249+24046G>C		intron	N/A	ENSP00000437621.1
	HMGA2	ENST00000354636.7	TSL:1	c.249+24046G>C		intron	N/A	ENSP00000346658.3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40474 AN: 152014 Hom.: 10842 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.267 AC: 40573 AN: 152132 Hom.: 10884 Cov.: 33 AF XY: 0.267 AC XY: 19841 AN XY: 74378

African (AFR) AF: 0.689 AC: 28580 AN: 41472

American (AMR) AF: 0.174 AC: 2654 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5178

South Asian (SAS) AF: 0.293 AC: 1415 AN: 4826

European-Finnish (FIN) AF: 0.0873 AC: 924 AN: 10586

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.0686 AC: 4667 AN: 68000

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.0428 Hom.: 61

Bravo AF: 0.289

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.39
PhyloP100		-1.8
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: rs11175944; hg19: chr12-66256395;