chr2-70514916-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003236.4(TGFA):c.41-4A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000513 in 1,613,660 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003236.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFA | NM_003236.4 | c.41-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000295400.11 | |||
TGFA | NM_001099691.3 | c.41-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TGFA | NM_001308158.2 | c.59-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TGFA | NM_001308159.2 | c.59-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFA | ENST00000295400.11 | c.41-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003236.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00287 AC: 436AN: 152120Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000813 AC: 203AN: 249798Hom.: 4 AF XY: 0.000496 AC XY: 67AN XY: 134998
GnomAD4 exome AF: 0.000268 AC: 392AN: 1461422Hom.: 4 Cov.: 31 AF XY: 0.000206 AC XY: 150AN XY: 726964
GnomAD4 genome ? AF: 0.00286 AC: 436AN: 152238Hom.: 3 Cov.: 32 AF XY: 0.00274 AC XY: 204AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at