1-200407718-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001281293.2(ZNF281):c.1988G>A(p.Ser663Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001281293.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF281 | NM_001281293.2 | c.1988G>A | p.Ser663Asn | missense_variant | Exon 2 of 2 | ENST00000367353.2 | NP_001268222.1 | |
ZNF281 | NM_012482.5 | c.1988G>A | p.Ser663Asn | missense_variant | Exon 2 of 2 | NP_036614.1 | ||
ZNF281 | NM_001281294.2 | c.1880G>A | p.Ser627Asn | missense_variant | Exon 3 of 3 | NP_001268223.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF281 | ENST00000367353.2 | c.1988G>A | p.Ser663Asn | missense_variant | Exon 2 of 2 | 1 | NM_001281293.2 | ENSP00000356322.1 | ||
ZNF281 | ENST00000294740.3 | c.1988G>A | p.Ser663Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000294740.2 | |||
ZNF281 | ENST00000367352.3 | c.1880G>A | p.Ser627Asn | missense_variant | Exon 3 of 3 | 2 | ENSP00000356321.3 | |||
ENSG00000230623 | ENST00000637430.1 | n.484+44190C>T | intron_variant | Intron 4 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251382Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135860
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461840Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727220
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1988G>A (p.S663N) alteration is located in exon 2 (coding exon 1) of the ZNF281 gene. This alteration results from a G to A substitution at nucleotide position 1988, causing the serine (S) at amino acid position 663 to be replaced by an asparagine (N). 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