2-70453272-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003236.4(TGFA):c.421G>A(p.Glu141Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,920 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003236.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFA | NM_003236.4 | c.421G>A | p.Glu141Lys | missense_variant | Exon 5 of 6 | ENST00000295400.11 | NP_003227.1 | |
TGFA | NM_001308158.2 | c.439G>A | p.Glu147Lys | missense_variant | Exon 5 of 6 | NP_001295087.1 | ||
TGFA | NM_001308159.2 | c.436G>A | p.Glu146Lys | missense_variant | Exon 5 of 6 | NP_001295088.1 | ||
TGFA | NM_001099691.3 | c.418G>A | p.Glu140Lys | missense_variant | Exon 5 of 6 | NP_001093161.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251316Hom.: 1 AF XY: 0.0000810 AC XY: 11AN XY: 135818
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461766Hom.: 1 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727170
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.421G>A (p.E141K) alteration is located in exon 5 (coding exon 5) of the TGFA gene. This alteration results from a G to A substitution at nucleotide position 421, causing the glutamic acid (E) at amino acid position 141 to be replaced by a lysine (K). 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