16-2831797-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_145252.3(ZG16B):c.157G>A(p.Val53Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000317 in 1,610,496 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145252.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZG16B | ENST00000382280.8 | c.157G>A | p.Val53Ile | missense_variant, splice_region_variant | 4/4 | 1 | NM_145252.3 | ENSP00000371715.4 | ||
ZG16B | ENST00000572863.2 | c.157G>A | p.Val53Ile | missense_variant, splice_region_variant | 3/3 | 2 | ENSP00000461740.2 | |||
ZG16B | ENST00000570670.6 | c.155+1001G>A | intron_variant | 3 | ENSP00000460793.2 | |||||
ZG16B | ENST00000573019.1 | n.409G>A | splice_region_variant, non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247074Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134202
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1458202Hom.: 1 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 724994
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at