16-30585145-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152458.7(ZNF785):c.311G>A(p.Ser104Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152458.7 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 |
---|---|---|---|---|---|---|---|
ZNF785 | NM_152458.7 | c.311G>A | p.Ser104Asn | missense_variant | 2/3 | ENST00000395216.3 | |
ZNF785 | XM_011545753.3 | c.350G>A | p.Ser117Asn | missense_variant | 2/4 | ||
ZNF785 | XM_017022967.3 | c.311G>A | p.Ser104Asn | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF785 | ENST00000395216.3 | c.311G>A | p.Ser104Asn | missense_variant | 2/3 | 1 | NM_152458.7 | P2 | |
ZNF785 | ENST00000567773.1 | c.*18G>A | 3_prime_UTR_variant | 2/3 | 4 | ||||
ZNF785 | ENST00000470110.2 | c.289+22G>A | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250688Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135548
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461124Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726760
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.311G>A (p.S104N) alteration is located in exon 2 (coding exon 2) of the ZNF785 gene. This alteration results from a G to A substitution at nucleotide position 311, causing the serine (S) at amino acid position 104 to be replaced by an asparagine (N). 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