8-37697566-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_025069.3(ZNF703):​c.665G>A​(p.Arg222His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,317,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

ZNF703
NM_025069.3 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.63
Variant links:
Genes affected
ZNF703 (HGNC:25883): (zinc finger protein 703) Predicted to enable DNA-binding transcription factor binding activity. Involved in several processes, including cellular response to estradiol stimulus; mammary gland epithelial cell differentiation; and positive regulation of mammary gland epithelial cell proliferation. Located in cytoplasm and nuclear matrix. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20889455).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF703NM_025069.3 linkc.665G>A p.Arg222His missense_variant 2/2 ENST00000331569.6 NP_079345.1 Q9H7S9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF703ENST00000331569.6 linkc.665G>A p.Arg222His missense_variant 2/21 NM_025069.3 ENSP00000332325.4 Q9H7S9

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000148
AC:
1
AN:
67600
Hom.:
0
AF XY:
0.0000272
AC XY:
1
AN XY:
36788
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.0000410
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000683
AC:
9
AN:
1317338
Hom.:
0
Cov.:
32
AF XY:
0.00000775
AC XY:
5
AN XY:
645312
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:
0.00000763
Gnomad4 OTH exome
AF:
0.0000183
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 06, 2023The c.665G>A (p.R222H) alteration is located in exon 2 (coding exon 2) of the ZNF703 gene. This alteration results from a G to A substitution at nucleotide position 665, causing the arginine (R) at amino acid position 222 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.018
T
Eigen
Benign
0.11
Eigen_PC
Benign
0.17
FATHMM_MKL
Benign
0.65
D
LIST_S2
Benign
0.81
T
M_CAP
Benign
0.072
D
MetaRNN
Benign
0.21
T
MetaSVM
Benign
-0.90
T
MutationAssessor
Benign
0.0
N
PrimateAI
Pathogenic
0.86
D
PROVEAN
Benign
-1.3
N
REVEL
Benign
0.054
Sift
Uncertain
0.023
D
Sift4G
Benign
0.11
T
Polyphen
0.97
D
Vest4
0.096
MutPred
0.33
Loss of methylation at R222 (P = 0.0149);
MVP
0.60
ClinPred
0.51
D
GERP RS
4.4
Varity_R
0.15
gMVP
0.14

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: rs1161883408; hg19: chr8-37555084; COSMIC: COSV58999015; API