rs141117763
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001079668.3(NKX2-1):c.*186_*187insCTACCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,026,644 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
NKX2-1
NM_001079668.3 3_prime_UTR
NM_001079668.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0890
Genes affected
NKX2-1 (HGNC:11825): (NK2 homeobox 1) This gene encodes a protein initially identified as a thyroid-specific transcription factor. The encoded protein binds to the thyroglobulin promoter and regulates the expression of thyroid-specific genes but has also been shown to regulate the expression of genes involved in morphogenesis. Mutations and deletions in this gene are associated with benign hereditary chorea, choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress, and may be associated with thyroid cancer. Multiple transcript variants encoding different isoforms have been found for this gene. This gene shares the symbol/alias 'TTF1' with another gene, transcription termination factor 1, which plays a role in ribosomal gene transcription. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NKX2-1 | NM_001079668.3 | c.*186_*187insCTACCC | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000354822.7 | NP_001073136.1 | ||
| NKX2-1 | NM_003317.4 | c.*186_*187insCTACCC | 3_prime_UTR_variant | Exon 2 of 2 | NP_003308.1 | |||
| SFTA3 | NR_161364.1 | n.89+2376_89+2377insCTACCC | intron_variant | Intron 1 of 4 | ||||
| SFTA3 | NR_161365.1 | n.89+2376_89+2377insCTACCC | intron_variant | Intron 1 of 4 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| NKX2-1 | ENST00000354822 | c.*186_*187insCTACCC | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_001079668.3 | ENSP00000346879.6 | |||
| SFTA3 | ENST00000546983.2 | n.373+1893_373+1894insCTACCC | intron_variant | Intron 2 of 3 | 4 | ENSP00000449302.2 |
Frequencies
GnomAD3 genomes 0.00000667 AC: 1AN: 149928Hom.: 0 Cov.: 28
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GnomAD4 exome AF: 0.00000684 AC: 6AN: 876716Hom.: 0 Cov.: 12 AF XY: 0.00000929 AC XY: 4AN XY: 430776
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GnomAD4 genome 0.00000667 AC: 1AN: 149928Hom.: 0 Cov.: 28 AF XY: 0.0000137 AC XY: 1AN XY: 72974
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at