chr21-42313614-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003226.4(TFF3):c.100G>A(p.Val34Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,610,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003226.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFF3 | ENST00000518498.3 | c.100G>A | p.Val34Met | missense_variant | Exon 2 of 3 | 1 | NM_003226.4 | ENSP00000430690.2 | ||
TFF3 | ENST00000398431.2 | c.105G>A | p.Pro35Pro | synonymous_variant | Exon 2 of 3 | 3 | ENSP00000381462.2 | |||
TFF3 | ENST00000489676.1 | n.73G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000444 AC: 11AN: 247734Hom.: 0 AF XY: 0.0000596 AC XY: 8AN XY: 134122
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1457924Hom.: 0 Cov.: 31 AF XY: 0.0000262 AC XY: 19AN XY: 725246
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.142G>A (p.V48M) alteration is located in exon 2 (coding exon 2) of the TFF3 gene. This alteration results from a G to A substitution at nucleotide position 142, causing the valine (V) at amino acid position 48 to be replaced by a methionine (M). 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