chr10-45618152-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_174890.4(ZFAND4):c.2036G>A(p.Ser679Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,612,162 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
ZFAND4
NM_174890.4 missense
NM_174890.4 missense
Scores
4
6
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.56
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFAND4 | NM_174890.4 | c.2036G>A | p.Ser679Asn | missense_variant | 9/10 | ENST00000344646.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFAND4 | ENST00000344646.10 | c.2036G>A | p.Ser679Asn | missense_variant | 9/10 | 1 | NM_174890.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249778Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135046
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1459954Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726256
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74358
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
0.96
.;D
Vest4
MVP
MPC
0.24
ClinPred
T
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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