rs71124756
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001079668.3(NKX2-1):c.*217delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000316 in 632,924 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: not found (cov: 21)
Exomes 𝑓: 0.0000032 ( 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: 0.476
Publications
0 publications found
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 was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NKX2-1 | NM_001079668.3 | c.*217delA | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000354822.7 | NP_001073136.1 | ||
| NKX2-1 | NM_003317.4 | c.*217delA | 3_prime_UTR_variant | Exon 2 of 2 | NP_003308.1 | |||
| SFTA3 | NR_161364.1 | n.89+2407delA | intron_variant | Intron 1 of 4 | ||||
| SFTA3 | NR_161365.1 | n.89+2407delA | intron_variant | Intron 1 of 4 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
21
GnomAD4 exome AF: 0.00000316 AC: 2AN: 632924Hom.: 0 Cov.: 10 AF XY: 0.00000315 AC XY: 1AN XY: 317210 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
632924
Hom.:
Cov.:
10
AF XY:
AC XY:
1
AN XY:
317210
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
17034
American (AMR)
AF:
AC:
0
AN:
12916
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12736
East Asian (EAS)
AF:
AC:
0
AN:
26010
South Asian (SAS)
AF:
AC:
0
AN:
40372
European-Finnish (FIN)
AF:
AC:
0
AN:
24212
Middle Eastern (MID)
AF:
AC:
0
AN:
2176
European-Non Finnish (NFE)
AF:
AC:
0
AN:
467330
Other (OTH)
AF:
AC:
1
AN:
30138
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
21
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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