chr12-121001057-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000545.8(HNF1A):c.1769-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000545.8 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C12orf43 | NM_022895.3 | c.*3096G>A | 3_prime_UTR_variant | 6/6 | ENST00000288757.7 | ||
HNF1A | NM_000545.8 | c.1769-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000257555.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C12orf43 | ENST00000288757.7 | c.*3096G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_022895.3 | P2 | ||
HNF1A | ENST00000257555.11 | c.1769-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000545.8 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460760Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726700
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at