chr1-117075281-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003594.4(TTF2):c.697T>C(p.Ser233Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003594.4 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 |
---|---|---|---|---|---|---|---|
TTF2 | NM_003594.4 | c.697T>C | p.Ser233Pro | missense_variant | 5/23 | ENST00000369466.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTF2 | ENST00000369466.9 | c.697T>C | p.Ser233Pro | missense_variant | 5/23 | 1 | NM_003594.4 | P1 | |
TTF2 | ENST00000470935.1 | n.686T>C | non_coding_transcript_exon_variant | 5/5 | 5 | ||||
TTF2 | ENST00000469638.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251068Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135824
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461892Hom.: 0 Cov.: 78 AF XY: 0.0000165 AC XY: 12AN XY: 727246
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.697T>C (p.S233P) alteration is located in exon 5 (coding exon 5) of the TTF2 gene. This alteration results from a T to C substitution at nucleotide position 697, causing the serine (S) at amino acid position 233 to be replaced by a proline (P). 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