chr16-31061887-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_024706.5(ZNF668):c.1041G>A(p.Ala347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,612,962 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00098 ( 18 hom. )
Consequence
ZNF668
NM_024706.5 synonymous
NM_024706.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.74
Genes affected
ZNF668 (HGNC:25821): (zinc finger protein 668) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 16-31061887-C-T is Benign according to our data. Variant chr16-31061887-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3043623.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.74 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000983 (1436/1460608) while in subpopulation EAS AF= 0.022 (873/39676). AF 95% confidence interval is 0.0208. There are 18 homozygotes in gnomad4_exome. There are 711 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF668 | NM_024706.5 | c.1041G>A | p.Ala347= | synonymous_variant | 3/3 | ENST00000300849.5 | |
ZNF668 | NM_001172669.2 | c.1110G>A | p.Ala370= | synonymous_variant | 4/4 | ||
ZNF668 | NM_001172668.2 | c.1041G>A | p.Ala347= | synonymous_variant | 3/3 | ||
ZNF668 | NM_001172670.2 | c.1041G>A | p.Ala347= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF668 | ENST00000300849.5 | c.1041G>A | p.Ala347= | synonymous_variant | 3/3 | 1 | NM_024706.5 | P1 | |
ENST00000622229.1 | n.2464C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00145 AC: 220AN: 152236Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00155 AC: 385AN: 248012Hom.: 3 AF XY: 0.00137 AC XY: 185AN XY: 134768
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GnomAD4 exome AF: 0.000983 AC: 1436AN: 1460608Hom.: 18 Cov.: 31 AF XY: 0.000979 AC XY: 711AN XY: 726574
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ZNF668-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at