2-70456379-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003236.4(TGFA):c.325G>A(p.Val109Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 1,572,908 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003236.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFA | NM_003236.4 | c.325G>A | p.Val109Met | missense_variant | 4/6 | ENST00000295400.11 | NP_003227.1 | |
TGFA | NM_001308158.2 | c.343G>A | p.Val115Met | missense_variant | 4/6 | NP_001295087.1 | ||
TGFA | NM_001308159.2 | c.340G>A | p.Val114Met | missense_variant | 4/6 | NP_001295088.1 | ||
TGFA | NM_001099691.3 | c.322G>A | p.Val108Met | missense_variant | 4/6 | NP_001093161.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGFA | ENST00000295400.11 | c.325G>A | p.Val109Met | missense_variant | 4/6 | 1 | NM_003236.4 | ENSP00000295400 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1675AN: 152214Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.00260 AC: 485AN: 186612Hom.: 7 AF XY: 0.00195 AC XY: 194AN XY: 99612
GnomAD4 exome AF: 0.00112 AC: 1587AN: 1420576Hom.: 28 Cov.: 31 AF XY: 0.000952 AC XY: 669AN XY: 702820
GnomAD4 genome AF: 0.0110 AC: 1678AN: 152332Hom.: 34 Cov.: 33 AF XY: 0.0103 AC XY: 770AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at