12-121000508-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022895.3(C12orf43):c.*3645G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 179,720 control chromosomes in the GnomAD database, including 10,655 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 0.32 ( 8732 hom., cov: 32)
Exomes 𝑓: 0.34 ( 1923 hom. )
Consequence
C12orf43
NM_022895.3 3_prime_UTR
NM_022895.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.14
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C12orf43 | NM_022895.3 | c.*3645G>A | 3_prime_UTR_variant | 6/6 | ENST00000288757.7 | NP_075046.1 | ||
HNF1A | NM_000545.8 | c.1769-557C>T | intron_variant | ENST00000257555.11 | NP_000536.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C12orf43 | ENST00000288757.7 | c.*3645G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_022895.3 | ENSP00000288757 | P2 | ||
HNF1A | ENST00000257555.11 | c.1769-557C>T | intron_variant | 1 | NM_000545.8 | ENSP00000257555 | P4 |
Frequencies
GnomAD3 genomes AF: 0.319 AC: 48533AN: 151934Hom.: 8728 Cov.: 32
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GnomAD4 exome AF: 0.343 AC: 9484AN: 27668Hom.: 1923 Cov.: 0 AF XY: 0.354 AC XY: 4979AN XY: 14072
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GnomAD4 genome AF: 0.319 AC: 48536AN: 152052Hom.: 8732 Cov.: 32 AF XY: 0.328 AC XY: 24398AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at