21-42350945-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005423.5(TFF2):c.13G>A(p.Asp5Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,613,980 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFF2 | ENST00000291526.5 | c.13G>A | p.Asp5Asn | missense_variant | Exon 1 of 4 | 1 | NM_005423.5 | ENSP00000291526.4 | ||
TFF2 | ENST00000463771.5 | n.53G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 5 | |||||
TFF2 | ENST00000475297.1 | n.50G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152246Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250902Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135666
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461616Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727138
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152364Hom.: 1 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13G>A (p.D5N) alteration is located in exon 1 (coding exon 1) of the TFF2 gene. This alteration results from a G to A substitution at nucleotide position 13, causing the aspartic acid (D) at amino acid position 5 to be replaced by an asparagine (N). 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