5-43175100-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001330707.2(ZNF131):āc.1839T>Gā(p.Asn613Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,016 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 (ā ).
Frequency
Consequence
NM_001330707.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF131 | NM_001330707.2 | c.1839T>G | p.Asn613Lys | missense_variant | 7/7 | ENST00000682664.1 | NP_001317636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF131 | ENST00000682664.1 | c.1839T>G | p.Asn613Lys | missense_variant | 7/7 | NM_001330707.2 | ENSP00000507111 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248872Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135128
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727166
GnomAD4 genome AF: 0.000112 AC: 17AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1737T>G (p.N579K) alteration is located in exon 8 (coding exon 7) of the ZNF131 gene. This alteration results from a T to G substitution at nucleotide position 1737, causing the asparagine (N) at amino acid position 579 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