chr16-30556107-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001172679.2(ZNF764):āc.311A>Gā(p.Asp104Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 1,610,534 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001172679.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
ZNF764 | NM_001172679.2 | c.311A>G | p.Asp104Gly | missense_variant, splice_region_variant | 3/3 | ENST00000395091.3 | |
ZNF764 | NM_033410.4 | c.314A>G | p.Asp105Gly | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF764 | ENST00000252797.6 | c.314A>G | p.Asp105Gly | missense_variant | 3/3 | 1 | P4 | ||
ZNF764 | ENST00000395091.3 | c.311A>G | p.Asp104Gly | missense_variant, splice_region_variant | 3/3 | 2 | NM_001172679.2 | A1 | |
ZNF764 | ENST00000568333.1 | n.480A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000224 AC: 56AN: 249808Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135274
GnomAD4 exome AF: 0.000359 AC: 523AN: 1458262Hom.: 1 Cov.: 33 AF XY: 0.000351 AC XY: 255AN XY: 725552
GnomAD4 genome AF: 0.000269 AC: 41AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.314A>G (p.D105G) alteration is located in exon 3 (coding exon 3) of the ZNF764 gene. This alteration results from a A to G substitution at nucleotide position 314, causing the aspartic acid (D) at amino acid position 105 to be replaced by a glycine (G). 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