chr10-47368636-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153034.4(ZNF488):c.194C>T(p.Ala65Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000287 in 1,603,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153034.4 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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF488 | NM_153034.4 | c.194C>T | p.Ala65Val | missense_variant | 2/2 | ENST00000585316.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF488 | ENST00000585316.3 | c.194C>T | p.Ala65Val | missense_variant | 2/2 | 1 | NM_153034.4 | A2 | |
ZNF488 | ENST00000591025.1 | c.-29+7C>T | splice_region_variant, intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151760Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000449 AC: 11AN: 244944Hom.: 0 AF XY: 0.0000601 AC XY: 8AN XY: 133204
GnomAD4 exome AF: 0.0000303 AC: 44AN: 1451304Hom.: 0 Cov.: 32 AF XY: 0.0000374 AC XY: 27AN XY: 722300
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151760Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74140
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 20, 2023 | The c.194C>T (p.A65V) alteration is located in exon 2 (coding exon 1) of the ZNF488 gene. This alteration results from a C to T substitution at nucleotide position 194, causing the alanine (A) at amino acid position 65 to be replaced by a valine (V). 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