chr19-51965309-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021632.4(ZNF350):c.1144G>A(p.Ala382Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021632.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF350 | NM_021632.4 | c.1144G>A | p.Ala382Thr | missense_variant | 5/5 | ENST00000243644.9 | NP_067645.3 | |
ZNF350-AS1 | NR_103847.1 | n.103-11082C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF350 | ENST00000243644.9 | c.1144G>A | p.Ala382Thr | missense_variant | 5/5 | 1 | NM_021632.4 | ENSP00000243644 | P1 | |
ZNF350-AS1 | ENST00000595010.4 | n.121-11082C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251218Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135788
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461724Hom.: 0 Cov.: 34 AF XY: 0.0000344 AC XY: 25AN XY: 727178
GnomAD4 genome AF: 0.000197 AC: 30AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 11, 2023 | The c.1144G>A (p.A382T) alteration is located in exon 5 (coding exon 4) of the ZNF350 gene. This alteration results from a G to A substitution at nucleotide position 1144, causing the alanine (A) at amino acid position 382 to be replaced by a threonine (T). 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