5-180849584-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001172638.2(ZFP62):c.1911G>T(p.Arg637Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,551,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R637K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001172638.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFP62 | ENST00000502412.2 | c.1911G>T | p.Arg637Ser | missense_variant | Exon 2 of 2 | 2 | NM_001172638.2 | ENSP00000423820.1 | ||
ZFP62 | ENST00000506377.5 | n.254-1502G>T | intron_variant | Intron 3 of 3 | 1 | |||||
ZFP62 | ENST00000512132.5 | c.1812G>T | p.Arg604Ser | missense_variant | Exon 3 of 3 | 2 | ENSP00000426193.1 | |||
ZFP62 | ENST00000507843.1 | n.-68G>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151952Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000316 AC: 5AN: 158350Hom.: 0 AF XY: 0.0000479 AC XY: 4AN XY: 83464
GnomAD4 exome AF: 0.0000243 AC: 34AN: 1399876Hom.: 0 Cov.: 78 AF XY: 0.0000275 AC XY: 19AN XY: 690414
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151952Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1911G>T (p.R637S) alteration is located in exon 2 (coding exon 2) of the ZFP62 gene. This alteration results from a G to T substitution at nucleotide position 1911, causing the arginine (R) at amino acid position 637 to be replaced by a serine (S). 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