chr19-57720533-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024833.3(ZNF671):c.1553G>A(p.Arg518Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024833.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF671 | NM_024833.3 | c.1553G>A | p.Arg518Gln | missense_variant | Exon 4 of 4 | ENST00000317398.10 | NP_079109.2 | |
ZNF671 | NM_001321376.2 | c.1322G>A | p.Arg441Gln | missense_variant | Exon 5 of 5 | NP_001308305.1 | ||
ZNF671 | NM_001321375.2 | c.1259G>A | p.Arg420Gln | missense_variant | Exon 3 of 3 | NP_001308304.1 | ||
ZNF671 | XM_017027314.2 | c.1322G>A | p.Arg441Gln | missense_variant | Exon 4 of 4 | XP_016882803.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF671 | ENST00000317398.10 | c.1553G>A | p.Arg518Gln | missense_variant | Exon 4 of 4 | 1 | NM_024833.3 | ENSP00000321848.5 | ||
ENSG00000269026 | ENST00000594684.1 | c.34-30252C>T | intron_variant | Intron 1 of 2 | 1 | ENSP00000472160.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251286Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135796
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461874Hom.: 0 Cov.: 34 AF XY: 0.0000426 AC XY: 31AN XY: 727230
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1553G>A (p.R518Q) alteration is located in exon 4 (coding exon 4) of the ZNF671 gene. This alteration results from a G to A substitution at nucleotide position 1553, causing the arginine (R) at amino acid position 518 to be replaced by a glutamine (Q). 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