11-1288704-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_019009.4(TOLLIP):c.439G>A(p.Val147Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,460,610 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V147E) has been classified as Uncertain significance.
Frequency
Consequence
NM_019009.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOLLIP | NM_019009.4 | c.439G>A | p.Val147Met | missense_variant | 4/6 | ENST00000317204.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOLLIP | ENST00000317204.11 | c.439G>A | p.Val147Met | missense_variant | 4/6 | 1 | NM_019009.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249952Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135542
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460610Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726624
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.439G>A (p.V147M) alteration is located in exon 4 (coding exon 4) of the TOLLIP gene. This alteration results from a G to A substitution at nucleotide position 439, causing the valine (V) at amino acid position 147 to be replaced by a methionine (M). 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