17-36486706-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004773.4(ZNHIT3):c.7T>A(p.Ser3Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004773.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNHIT3 | NM_004773.4 | c.7T>A | p.Ser3Thr | missense_variant | 1/5 | ENST00000617429.5 | |
LOC105371749 | XR_934710.4 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNHIT3 | ENST00000617429.5 | c.7T>A | p.Ser3Thr | missense_variant | 1/5 | 1 | NM_004773.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135768
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461640Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0AN XY: 727150
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
PEHO syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Apr 06, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at