rs146686581
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000545.8(HNF1A):c.210C>T(p.Ser70Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,607,956 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000545.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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HNF1A | NM_000545.8 | c.210C>T | p.Ser70Ser | synonymous_variant | Exon 1 of 10 | ENST00000257555.11 | NP_000536.6 | |
HNF1A | NM_001306179.2 | c.210C>T | p.Ser70Ser | synonymous_variant | Exon 1 of 10 | NP_001293108.2 | ||
HNF1A | NM_001406915.1 | c.210C>T | p.Ser70Ser | synonymous_variant | Exon 1 of 9 | NP_001393844.1 | ||
HNF1A | XM_024449168.2 | c.210C>T | p.Ser70Ser | synonymous_variant | Exon 1 of 9 | XP_024304936.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF1A | ENST00000257555.11 | c.210C>T | p.Ser70Ser | synonymous_variant | Exon 1 of 10 | 1 | NM_000545.8 | ENSP00000257555.5 |
Frequencies
GnomAD3 genomes AF: 0.000546 AC: 83AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 38AN: 232178Hom.: 0 AF XY: 0.000142 AC XY: 18AN XY: 126504
GnomAD4 exome AF: 0.0000701 AC: 102AN: 1455776Hom.: 3 Cov.: 35 AF XY: 0.0000815 AC XY: 59AN XY: 723722
GnomAD4 genome AF: 0.000545 AC: 83AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000565 AC XY: 42AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:2Other:1
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Maturity onset diabetes mellitus in young Benign:2
Mutations in HNF1A gene can predispose to MODY3. It is associated with both micro and macrovascular complications of diabetes, especially cardiovascular complications. Associated with glucosuria. May respond well to sulfonylureas. However, more evidence is required to confer the association of this particular variant rs146686581 with MODY3. -
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Nonpapillary renal cell carcinoma Benign:1
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not provided Benign:1
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Maturity-onset diabetes of the young type 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at