21-42347599-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005423.5(TFF2):c.263G>T(p.Arg88Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005423.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFF2 | ENST00000291526.5 | c.263G>T | p.Arg88Leu | missense_variant | Exon 3 of 4 | 1 | NM_005423.5 | ENSP00000291526.4 | ||
TFF2 | ENST00000463771.5 | n.266G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 | |||||
TFF2 | ENST00000475297.1 | n.393G>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251398Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135884
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727232
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.263G>T (p.R88L) alteration is located in exon 3 (coding exon 3) of the TFF2 gene. This alteration results from a G to T substitution at nucleotide position 263, causing the arginine (R) at amino acid position 88 to be replaced by a leucine (L). 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