chrX-15790512-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005089.4(ZRSR2):āc.17A>Cā(p.Lys6Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 1,158,629 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005089.4 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZRSR2 | NM_005089.4 | c.17A>C | p.Lys6Thr | missense_variant | 1/11 | ENST00000307771.8 | NP_005080.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZRSR2 | ENST00000307771.8 | c.17A>C | p.Lys6Thr | missense_variant | 1/11 | 1 | NM_005089.4 | ENSP00000303015.7 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111969Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34153
GnomAD4 exome AF: 0.0000287 AC: 30AN: 1046660Hom.: 0 Cov.: 31 AF XY: 0.0000383 AC XY: 13AN XY: 339296
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111969Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34153
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2024 | The c.17A>C (p.K6T) alteration is located in exon 1 (coding exon 1) of the ZRSR2 gene. This alteration results from a A to C substitution at nucleotide position 17, causing the lysine (K) at amino acid position 6 to be replaced by a threonine (T). 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