rs760492866

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_017757.3(ZNF407):​c.4010A>C​(p.Tyr1337Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

ZNF407
NM_017757.3 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.07
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.42366546).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF407NM_017757.3 linkc.4010A>C p.Tyr1337Ser missense_variant Exon 2 of 9 ENST00000299687.10 NP_060227.2 Q9C0G0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF407ENST00000299687.10 linkc.4010A>C p.Tyr1337Ser missense_variant Exon 2 of 9 1 NM_017757.3 ENSP00000299687.4 Q9C0G0-1
ZNF407ENST00000577538.5 linkc.4010A>C p.Tyr1337Ser missense_variant Exon 1 of 7 2 ENSP00000463270.1 Q9C0G0-2
ZNF407ENST00000309902.10 linkc.4010A>C p.Tyr1337Ser missense_variant Exon 1 of 4 2 ENSP00000310359.5 Q9C0G0-3
ZNF407ENST00000582337.5 linkc.4010A>C p.Tyr1337Ser missense_variant Exon 2 of 5 5 ENSP00000462348.1 Q9C0G0-3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461676
Hom.:
0
Cov.:
41
AF XY:
0.00000138
AC XY:
1
AN XY:
727122
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
ExAC
AF:
0.00000827
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
0.011
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.057
.;.;.;T
Eigen
Benign
0.14
Eigen_PC
Benign
0.14
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.68
.;T;T;T
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.42
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.5
M;M;M;M
PrimateAI
Benign
0.43
T
PROVEAN
Uncertain
-2.5
.;D;.;N
REVEL
Benign
0.17
Sift
Benign
0.034
.;D;.;D
Sift4G
Benign
0.17
T;T;T;T
Polyphen
1.0
D;D;D;D
Vest4
0.50
MutPred
0.62
Gain of disorder (P = 0.0014);Gain of disorder (P = 0.0014);Gain of disorder (P = 0.0014);Gain of disorder (P = 0.0014);
MVP
0.29
MPC
0.42
ClinPred
0.94
D
GERP RS
4.6
Varity_R
0.16
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs760492866; hg19: chr18-72346985; API