1-42851623-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242739.2(ZNF691):c.758G>A(p.Arg253Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,892 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001242739.2 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 |
---|---|---|---|---|---|---|---|
ZNF691 | NM_001242739.2 | c.758G>A | p.Arg253Lys | missense_variant | 4/4 | ENST00000651192.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF691 | ENST00000651192.1 | c.758G>A | p.Arg253Lys | missense_variant | 4/4 | NM_001242739.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251194Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135784
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461882Hom.: 1 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.758G>A (p.R253K) alteration is located in exon 4 (coding exon 2) of the ZNF691 gene. This alteration results from a G to A substitution at nucleotide position 758, causing the arginine (R) at amino acid position 253 to be replaced by a lysine (K). 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