3-42658711-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145166.4(ZBTB47):c.356C>T(p.Pro119Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 1,535,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145166.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZBTB47 | NM_145166.4 | c.356C>T | p.Pro119Leu | missense_variant | Exon 2 of 6 | ENST00000232974.11 | NP_660149.2 | |
ZBTB47 | NM_001410746.1 | c.440C>T | p.Pro147Leu | missense_variant | Exon 2 of 6 | NP_001397675.1 | ||
ZBTB47 | XM_047449234.1 | c.536C>T | p.Pro179Leu | missense_variant | Exon 3 of 7 | XP_047305190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZBTB47 | ENST00000232974.11 | c.356C>T | p.Pro119Leu | missense_variant | Exon 2 of 6 | 5 | NM_145166.4 | ENSP00000232974.6 | ||
ZBTB47 | ENST00000680014.1 | c.440C>T | p.Pro147Leu | missense_variant | Exon 2 of 6 | ENSP00000504903.1 | ||||
ZBTB47 | ENST00000505904.1 | c.-421C>T | upstream_gene_variant | 5 | ENSP00000420968.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000644 AC: 9AN: 139738Hom.: 0 AF XY: 0.0000665 AC XY: 5AN XY: 75178
GnomAD4 exome AF: 0.0000152 AC: 21AN: 1382982Hom.: 0 Cov.: 32 AF XY: 0.0000132 AC XY: 9AN XY: 682374
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.356C>T (p.P119L) alteration is located in exon 2 (coding exon 1) of the ZBTB47 gene. This alteration results from a C to T substitution at nucleotide position 356, causing the proline (P) at amino acid position 119 to be replaced by a leucine (L). 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