10-99535546-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_145285.3(NKX2-3):c.920C>T(p.Ser307Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,396,270 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145285.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX2-3 | NM_145285.3 | c.920C>T | p.Ser307Phe | missense_variant | 2/2 | ENST00000344586.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX2-3 | ENST00000344586.9 | c.920C>T | p.Ser307Phe | missense_variant | 2/2 | 2 | NM_145285.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 4AN: 150816Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000128 AC: 159AN: 1245454Hom.: 3 Cov.: 33 AF XY: 0.000129 AC XY: 79AN XY: 610946
GnomAD4 genome ? AF: 0.0000265 AC: 4AN: 150816Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73618
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.920C>T (p.S307F) alteration is located in exon 2 (coding exon 2) of the NKX2-3 gene. This alteration results from a C to T substitution at nucleotide position 920, causing the serine (S) at amino acid position 307 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at