NM_145899.3:c.*1207A>T

Variant names:

• chr6-34246091-A-T
• rs1150782
• NM_145899.3:c.*1207A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_145899.3(HMGA1):​c.*1207A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HMGA1 NM_145899.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 publications found

Genes affected

HMGA1 (HGNC:5010): (high mobility group AT-hook 1) This gene encodes a chromatin-associated protein involved in the regulation of gene transcription, integration of retroviruses into chromosomes, and the metastatic progression of cancer cells. The encoded protein preferentially binds to the minor groove of AT-rich regions in double-stranded DNA. Multiple transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene have been identified on multiple chromosomes. [provided by RefSeq, Jan 2016]

HMGA1 Gene-Disease associations (from GenCC):

• type 2 diabetes mellitus

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145899.3. 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
	HMGA1	NM_145899.3	MANE Select	c.*1207A>T		3_prime_UTR	Exon 6 of 6	NP_665906.1
	HMGA1	NM_001319078.2		c.*1207A>T		3_prime_UTR	Exon 5 of 5	NP_001306007.1
	HMGA1	NM_001319079.2		c.*1207A>T		3_prime_UTR	Exon 6 of 6	NP_001306008.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGA1	ENST00000311487.9	TSL:1 MANE Select	c.*1207A>T		3_prime_UTR	Exon 6 of 6	ENSP00000308227.4
	HMGA1	ENST00000447654.5	TSL:1	c.*1207A>T		3_prime_UTR	Exon 5 of 5	ENSP00000399888.1
	HMGA1	ENST00000347617.10	TSL:1	c.*1207A>T		3_prime_UTR	Exon 5 of 5	ENSP00000288245.9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 85638 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 40648

African (AFR) AF: 0.00 AC: 0 AN: 3330

American (AMR) AF: 0.00 AC: 0 AN: 3408

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4616

East Asian (EAS) AF: 0.00 AC: 0 AN: 10338

South Asian (SAS) AF: 0.00 AC: 0 AN: 2818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 916

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 448

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53084

Other (OTH) AF: 0.00 AC: 0 AN: 6680

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.67
PhyloP100		-1.6

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: rs1150782; hg19: chr6-34213868;