12-65963237-TGTTCCAG-T

Position:

• chr12-65963237-TGTTCCAG-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_Strong PM2 PP5

The NM_003483.6(HMGA2):​c.283-6_283delTTCCAGG​(p.Glu95fs) variant causes a frameshift, splice acceptor, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 31)
• Consequence: HMGA2 NM_003483.6 frameshift, splice_acceptor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 7.05

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.142 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-65963237-TGTTCCAG-T is Pathogenic according to our data. Variant chr12-65963237-TGTTCCAG-T is described in ClinVar as [Pathogenic]. Clinvar id is 917504.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr12-65963237-TGTTCCAG-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMGA2	NM_003483.6	c.283-6_283delTTCCAGG	p.Glu95fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	5/5	ENST00000403681.7	NP_003474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HMGA2	ENST00000403681.7	c.283-6_283delTTCCAGG	p.Glu95fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	5/5	1	NM_003483.6	ENSP00000384026.2
HMGA2	ENST00000539662.1	n.*152-6_*152delTTCCAGG		splice_region_variant, non_coding_transcript_exon_variant	5/5	3		ENSP00000440919.1
HMGA2	ENST00000539662.1	n.*152-6_*152delTTCCAGG		splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant	5/5	3		ENSP00000440919.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Silver-Russell syndrome 5 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 12, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1876803958; hg19: chr12-66357017;