19-57720543-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.1543G>A(p.Glu515Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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
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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.1543G>A | p.Glu515Lys | missense_variant | Exon 4 of 4 | ENST00000317398.10 | NP_079109.2 | |
ZNF671 | NM_001321376.2 | c.1312G>A | p.Glu438Lys | missense_variant | Exon 5 of 5 | NP_001308305.1 | ||
ZNF671 | NM_001321375.2 | c.1249G>A | p.Glu417Lys | missense_variant | Exon 3 of 3 | NP_001308304.1 | ||
ZNF671 | XM_017027314.2 | c.1312G>A | p.Glu438Lys | 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.1543G>A | p.Glu515Lys | missense_variant | Exon 4 of 4 | 1 | NM_024833.3 | ENSP00000321848.5 | ||
ENSG00000269026 | ENST00000594684.1 | c.34-30242C>T | intron_variant | Intron 1 of 2 | 1 | ENSP00000472160.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251314Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135812
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461888Hom.: 0 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1543G>A (p.E515K) 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 1543, causing the glutamic acid (E) at amino acid position 515 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