6-34856353-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017754.4(BLTP3A):c.1235C>T(p.Thr412Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017754.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLTP3A | NM_017754.4 | c.1235C>T | p.Thr412Met | missense_variant | 10/21 | ENST00000192788.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLTP3A | ENST00000192788.6 | c.1235C>T | p.Thr412Met | missense_variant | 10/21 | 1 | NM_017754.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000882 AC: 22AN: 249432Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135310
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727230
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1235C>T (p.T412M) alteration is located in exon 10 (coding exon 10) of the UHRF1BP1 gene. This alteration results from a C to T substitution at nucleotide position 1235, causing the threonine (T) at amino acid position 412 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