chr1-117075435-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003594.4(TTF2):c.851A>T(p.Glu284Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,052 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.851A>T | p.Glu284Val | missense_variant | 5/23 | ENST00000369466.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTF2 | ENST00000369466.9 | c.851A>T | p.Glu284Val | missense_variant | 5/23 | 1 | NM_003594.4 | P1 | |
TTF2 | ENST00000469638.1 | n.141A>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
TTF2 | ENST00000470935.1 | n.840A>T | non_coding_transcript_exon_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251342Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135858
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461838Hom.: 0 Cov.: 78 AF XY: 0.0000248 AC XY: 18AN XY: 727214
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.851A>T (p.E284V) alteration is located in exon 5 (coding exon 5) of the TTF2 gene. This alteration results from a A to T substitution at nucleotide position 851, causing the glutamic acid (E) at amino acid position 284 to be replaced by a valine (V). 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