12-121000906-G-GTTAAGAACCGAGGGAGCCTCCCAGCCAGGGAGGCTCCCTTTGTT

Variant names:

• chr12-121000906-G-GTTAAGAACCGAGGGAGCCTCCCAGCCAGGGAGGCTCCCTTTGTT
• rs3999412
• NM_022895.3:c.*3246_*3247insAACAAAGGGAGCCTCCCTGGCTGGGAGGCTCCCTCGGTTCTTAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_022895.3(C12orf43):​c.*3246_*3247insAACAAAGGGAGCCTCCCTGGCTGGGAGGCTCCCTCGGTTCTTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: C12orf43 NM_022895.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

C12orf43 (HGNC:25719): (chromosome 12 open reading frame 43) Predicted to be involved in Spemann organizer formation and negative regulation of Wnt signaling pathway. Predicted to be located in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

HNF1A (HGNC:11621): (HNF1 homeobox A) The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf43	NM_022895.3	c.*3246_*3247insAACAAAGGGAGCCTCCCTGGCTGGGAGGCTCCCTCGGTTCTTAA		3_prime_UTR_variant	Exon 6 of 6	ENST00000288757.7	NP_075046.1
HNF1A	NM_000545.8	c.1769-159_1769-158insTTAAGAACCGAGGGAGCCTCCCAGCCAGGGAGGCTCCCTTTGTT		intron_variant	Intron 9 of 9	ENST00000257555.11	NP_000536.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf43	ENST00000288757	c.*3246_*3247insAACAAAGGGAGCCTCCCTGGCTGGGAGGCTCCCTCGGTTCTTAA		3_prime_UTR_variant	Exon 6 of 6	1	NM_022895.3	ENSP00000288757.5
HNF1A	ENST00000257555.11	c.1769-159_1769-158insTTAAGAACCGAGGGAGCCTCCCAGCCAGGGAGGCTCCCTTTGTT		intron_variant	Intron 9 of 9	1	NM_000545.8	ENSP00000257555.5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 12

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

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: rs3999412; hg19: chr12-121438709;