3-52229058-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_007284.4(TWF2):c.1026G>A(p.Pro342Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007284.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TWF2 | ENST00000305533.10 | c.1026G>A | p.Pro342Pro | synonymous_variant | Exon 9 of 9 | 1 | NM_007284.4 | ENSP00000303908.4 | ||
ENSG00000173366 | ENST00000494383.1 | c.462+603G>A | intron_variant | Intron 4 of 4 | 2 | ENSP00000417517.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250532Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135512
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1459830Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726266
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74520
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at