rs183815209

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7

The ENST00000299687.10(ZNF407):​c.5589G>A​(p.Val1863=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,613,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

ZNF407
ENST00000299687.10 synonymous

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: -0.474
Variant links:
Genes affected
ZNF407 (HGNC:19904): (zinc finger protein 407) This gene encodes a zinc finger protein whose exact function is not known. It may be involved in transcriptional regulation. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 18-75063310-G-A is Benign according to our data. Variant chr18-75063310-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 212674.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=-0.474 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF407NM_017757.3 linkuse as main transcriptc.5589G>A p.Val1863= synonymous_variant 9/9 ENST00000299687.10 NP_060227.2
ZNF407NM_001384475.1 linkuse as main transcriptc.5589G>A p.Val1863= synonymous_variant 9/9 NP_001371404.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF407ENST00000299687.10 linkuse as main transcriptc.5589G>A p.Val1863= synonymous_variant 9/91 NM_017757.3 ENSP00000299687 P2Q9C0G0-1
ZNF407ENST00000579200.1 linkuse as main transcriptn.2029G>A non_coding_transcript_exon_variant 1/1
ZNF407ENST00000582214.1 linkuse as main transcriptn.307G>A non_coding_transcript_exon_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.00118
AC:
180
AN:
152190
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00420
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000317
AC:
78
AN:
246336
Hom.:
0
AF XY:
0.000239
AC XY:
32
AN XY:
133928
show subpopulations
Gnomad AFR exome
AF:
0.00498
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000142
AC:
208
AN:
1461356
Hom.:
0
Cov.:
29
AF XY:
0.000120
AC XY:
87
AN XY:
726962
show subpopulations
Gnomad4 AFR exome
AF:
0.00559
Gnomad4 AMR exome
AF:
0.0000894
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.00117
AC:
178
AN:
152308
Hom.:
0
Cov.:
32
AF XY:
0.00118
AC XY:
88
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.00414
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00185
Hom.:
0
Bravo
AF:
0.00148

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoJan 12, 2015- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
CADD
Benign
1.1
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs183815209; hg19: chr18-72775266; API