chr14-36517871-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_001079668.3(NKX2-1):āc.613G>Cā(p.Glu205Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,611,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E205E) has been classified as Likely benign.
Frequency
Consequence
NM_001079668.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKX2-1 | NM_001079668.3 | c.613G>C | p.Glu205Gln | missense_variant | 3/3 | ENST00000354822.7 | |
SFTA3 | NR_161364.1 | n.89+1597G>C | intron_variant, non_coding_transcript_variant | ||||
NKX2-1 | NM_003317.4 | c.523G>C | p.Glu175Gln | missense_variant | 2/2 | ||
SFTA3 | NR_161365.1 | n.89+1597G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKX2-1 | ENST00000354822.7 | c.613G>C | p.Glu205Gln | missense_variant | 3/3 | 1 | NM_001079668.3 | P4 | |
ENST00000634305.1 | n.322+69034C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244322Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132794
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459454Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 725958
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74506
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at