chr11-113738269-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004724.4(ZW10):c.1879C>T(p.Arg627Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000685 in 1,604,980 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R627Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004724.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZW10 | NM_004724.4 | c.1879C>T | p.Arg627Trp | missense_variant | 13/16 | ENST00000200135.8 | |
ZW10 | XM_017018558.3 | c.1687C>T | p.Arg563Trp | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZW10 | ENST00000200135.8 | c.1879C>T | p.Arg627Trp | missense_variant | 13/16 | 1 | NM_004724.4 | P1 | |
ZW10 | ENST00000535142.5 | c.1879C>T | p.Arg627Trp | missense_variant, NMD_transcript_variant | 13/16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151884Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000823 AC: 20AN: 243154Hom.: 0 AF XY: 0.000106 AC XY: 14AN XY: 131482
GnomAD4 exome AF: 0.0000702 AC: 102AN: 1453096Hom.: 0 Cov.: 31 AF XY: 0.0000761 AC XY: 55AN XY: 722650
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151884Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.1879C>T (p.R627W) alteration is located in exon 13 (coding exon 13) of the ZW10 gene. This alteration results from a C to T substitution at nucleotide position 1879, causing the arginine (R) at amino acid position 627 to be replaced by a tryptophan (W). 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