chr6-151366528-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020861.3(ZBTB2):āc.538C>Gā(p.Leu180Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,614,038 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 (ā ).
Frequency
Consequence
NM_020861.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB2 | NM_020861.3 | c.538C>G | p.Leu180Val | missense_variant | 3/3 | ENST00000325144.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB2 | ENST00000325144.5 | c.538C>G | p.Leu180Val | missense_variant | 3/3 | 1 | NM_020861.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251444Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135902
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000770 AC XY: 56AN XY: 727246
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2023 | The c.538C>G (p.L180V) alteration is located in exon 3 (coding exon 2) of the ZBTB2 gene. This alteration results from a C to G substitution at nucleotide position 538, causing the leucine (L) at amino acid position 180 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