5-150896637-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052860.4(ZNF300):c.602C>T(p.Pro201Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,366 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_052860.4 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 |
---|---|---|---|---|---|---|---|
ZNF300 | NM_052860.4 | c.602C>T | p.Pro201Leu | missense_variant | 6/6 | ENST00000274599.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF300 | ENST00000274599.10 | c.602C>T | p.Pro201Leu | missense_variant | 6/6 | 1 | NM_052860.4 | P1 | |
ZNF300 | ENST00000446148.7 | c.602C>T | p.Pro201Leu | missense_variant | 7/7 | 1 | P1 | ||
IRGM | ENST00000520549.1 | c.*141-3952G>A | intron_variant, NMD_transcript_variant | 1 | |||||
ZNF300 | ENST00000427179.5 | c.*1417C>T | 3_prime_UTR_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 151944Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250602Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135522
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461304Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 726950
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.650C>T (p.P217L) alteration is located in exon 7 (coding exon 5) of the ZNF300 gene. This alteration results from a C to T substitution at nucleotide position 650, causing the proline (P) at amino acid position 217 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