rs192918926
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014797.3(ZBTB24):c.14C>T(p.Ser5Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,614,118 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S5S) has been classified as Likely benign.
Frequency
Consequence
NM_014797.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB24 | NM_014797.3 | c.14C>T | p.Ser5Leu | missense_variant | 2/7 | ENST00000230122.4 | |
ZBTB24 | NM_001164313.2 | c.14C>T | p.Ser5Leu | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB24 | ENST00000230122.4 | c.14C>T | p.Ser5Leu | missense_variant | 2/7 | 1 | NM_014797.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000850 AC: 211AN: 248370Hom.: 1 AF XY: 0.000778 AC XY: 105AN XY: 134912
GnomAD4 exome AF: 0.000180 AC: 263AN: 1461838Hom.: 3 Cov.: 31 AF XY: 0.000195 AC XY: 142AN XY: 727220
GnomAD4 genome ? AF: 0.000473 AC: 72AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74440
ClinVar
Submissions by phenotype
Immunodeficiency-centromeric instability-facial anomalies syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 16, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | ZBTB24: BP4, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at