rs1169293
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000545.8(HNF1A):c.327-91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 1,153,512 control chromosomes in the GnomAD database, including 489,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.90 ( 61428 hom., cov: 33)
Exomes 𝑓: 0.92 ( 427939 hom. )
Consequence
HNF1A
NM_000545.8 intron
NM_000545.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.297
Genes affected
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 12-120988742-G-A is Benign according to our data. Variant chr12-120988742-G-A is described in ClinVar as [Benign]. Clinvar id is 1232183.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-120988742-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF1A | NM_000545.8 | c.327-91G>A | intron_variant | ENST00000257555.11 | |||
HNF1A | NM_001306179.2 | c.327-91G>A | intron_variant | ||||
HNF1A | NM_001406915.1 | c.327-91G>A | intron_variant | ||||
HNF1A | XM_024449168.2 | c.327-91G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF1A | ENST00000257555.11 | c.327-91G>A | intron_variant | 1 | NM_000545.8 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.897 AC: 136383AN: 152084Hom.: 61375 Cov.: 33
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GnomAD4 exome AF: 0.924 AC: 925122AN: 1001310Hom.: 427939 AF XY: 0.922 AC XY: 472522AN XY: 512504
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GnomAD4 genome ? AF: 0.897 AC: 136496AN: 152202Hom.: 61428 Cov.: 33 AF XY: 0.898 AC XY: 66800AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
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CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at