chrX-47915929-C-T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007137.5(ZNF81):c.1283C>T(p.Thr428Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000729 in 1,097,426 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_007137.5 missense
Scores
Clinical Significance
Conservation
Publications
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
- intellectual disability, X-linked 45Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
- X-linked intellectual disabilityInheritance: XL Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF81 | ENST00000338637.13 | c.1283C>T | p.Thr428Ile | missense_variant | Exon 5 of 5 | 3 | NM_007137.5 | ENSP00000341151.7 | ||
ZNF81 | ENST00000376954.6 | c.1283C>T | p.Thr428Ile | missense_variant | Exon 6 of 6 | 5 | ENSP00000366153.1 | |||
ZNF81 | ENST00000376950.4 | c.277+19989C>T | intron_variant | Intron 4 of 4 | 5 | ENSP00000366149.4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 110855Hom.: 0 Cov.: 22
GnomAD2 exomes AF: 0.00000554 AC: 1AN: 180607 AF XY: 0.0000151 show subpopulations
GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097426Hom.: 0 Cov.: 32 AF XY: 0.00000827 AC XY: 3AN XY: 362924 show subpopulations
Age Distribution
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 110855Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33195
ClinVar
Submissions by phenotype
not specified Uncertain:2
The c.1283C>T (p.T428I) alteration is located in exon 5 (coding exon 4) of the ZNF81 gene. This alteration results from a C to T substitution at nucleotide position 1283, causing the threonine (T) at amino acid position 428 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at