1-53894492-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PS1_ModeratePP5BP4BS2
The NM_000792.7(DIO1):c.282C>A(p.Asn94Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_000792.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIO1 | NM_000792.7 | c.282C>A | p.Asn94Lys | missense_variant | 1/4 | ENST00000361921.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIO1 | ENST00000361921.8 | c.282C>A | p.Asn94Lys | missense_variant | 1/4 | 1 | NM_000792.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249008Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134800
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727248
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
Thyroid hormone metabolism, abnormal, 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at