chr19-7916623-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195259.2(TGFBR3L):c.278C>T(p.Ala93Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000831 in 1,419,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001195259.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFBR3L | NM_001195259.2 | c.278C>T | p.Ala93Val | missense_variant, splice_region_variant | Exon 2 of 6 | ENST00000565886.2 | NP_001182188.1 | |
TGFBR3L | XM_011527610.3 | c.356C>T | p.Ala119Val | missense_variant | Exon 1 of 4 | XP_011525912.1 | ||
TGFBR3L | XM_011527613.3 | c.356C>T | p.Ala119Val | missense_variant | Exon 1 of 5 | XP_011525915.1 | ||
TGFBR3L | NM_001419781.1 | c.206C>T | p.Ala69Val | missense_variant, splice_region_variant | Exon 3 of 7 | NP_001406710.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000200 AC: 7AN: 34932Hom.: 0 AF XY: 0.000274 AC XY: 5AN XY: 18272
GnomAD4 exome AF: 0.0000813 AC: 103AN: 1267680Hom.: 0 Cov.: 31 AF XY: 0.000101 AC XY: 62AN XY: 616098
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152118Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.278C>T (p.A93V) alteration is located in exon 2 (coding exon 2) of the TGFBR3L gene. This alteration results from a C to T substitution at nucleotide position 278, causing the alanine (A) at amino acid position 93 to be replaced by a valine (V). 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