17-36171907-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001001417.7(TBC1D3B):c.445A>G(p.Ile149Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 149,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001001417.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D3B | ENST00000611257.5 | c.445A>G | p.Ile149Val | missense_variant | Exon 7 of 14 | 1 | NM_001001417.7 | ENSP00000478473.1 | ||
TBC1D3B | ENST00000622280.1 | n.417A>G | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | |||||
ENSG00000276241 | ENST00000617914.1 | n.158-5288T>C | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000134 AC: 20AN: 149176Hom.: 0 Cov.: 24
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000640 AC: 93AN: 1453672Hom.: 6 Cov.: 33 AF XY: 0.0000802 AC XY: 58AN XY: 723392
GnomAD4 genome AF: 0.000134 AC: 20AN: 149292Hom.: 0 Cov.: 24 AF XY: 0.000110 AC XY: 8AN XY: 72906
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at