chr2-179769594-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_152520.6(ZNF385B):c.207C>T(p.Asn69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0057 in 1,614,136 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0046 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0058 ( 25 hom. )
Consequence
ZNF385B
NM_152520.6 synonymous
NM_152520.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.525
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 2-179769594-G-A is Benign according to our data. Variant chr2-179769594-G-A is described in ClinVar as [Benign]. Clinvar id is 774598.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.525 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF385B | NM_152520.6 | c.207C>T | p.Asn69= | synonymous_variant | 3/10 | ENST00000410066.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF385B | ENST00000410066.7 | c.207C>T | p.Asn69= | synonymous_variant | 3/10 | 1 | NM_152520.6 | P1 | |
ZNF385B | ENST00000451732.6 | c.207C>T | p.Asn69= | synonymous_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00459 AC: 698AN: 152130Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00388 AC: 975AN: 251406Hom.: 6 AF XY: 0.00400 AC XY: 543AN XY: 135890
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GnomAD4 exome AF: 0.00581 AC: 8494AN: 1461888Hom.: 25 Cov.: 32 AF XY: 0.00565 AC XY: 4112AN XY: 727244
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GnomAD4 genome ? AF: 0.00459 AC: 699AN: 152248Hom.: 6 Cov.: 32 AF XY: 0.00466 AC XY: 347AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at