19-35715168-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014383.3(ZBTB32):c.542C>T(p.Thr181Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,424 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_014383.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZBTB32 | NM_014383.3 | c.542C>T | p.Thr181Met | missense_variant | Exon 3 of 7 | ENST00000392197.7 | NP_055198.1 | |
ZBTB32 | NM_001316902.2 | c.6-295C>T | intron_variant | Intron 2 of 6 | NP_001303831.1 | |||
ZBTB32 | NM_001316903.2 | c.-86-295C>T | intron_variant | Intron 2 of 5 | NP_001303832.1 | |||
ZBTB32 | XM_017026591.2 | c.6-295C>T | intron_variant | Intron 2 of 5 | XP_016882080.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZBTB32 | ENST00000392197.7 | c.542C>T | p.Thr181Met | missense_variant | Exon 3 of 7 | 5 | NM_014383.3 | ENSP00000376035.1 | ||
ZBTB32 | ENST00000262630.7 | c.542C>T | p.Thr181Met | missense_variant | Exon 2 of 6 | 1 | ENSP00000262630.3 | |||
ZBTB32 | ENST00000481182.1 | n.542C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 1 | ENSP00000433657.1 | ||||
ZBTB32 | ENST00000426659.6 | c.-86-295C>T | intron_variant | Intron 2 of 5 | 3 | ENSP00000466524.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152076Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250516Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135450
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461348Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726968
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152076Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.542C>T (p.T181M) alteration is located in exon 2 (coding exon 1) of the ZBTB32 gene. This alteration results from a C to T substitution at nucleotide position 542, causing the threonine (T) at amino acid position 181 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