rs1106499

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181489.6(ZNF445):​c.429+1172A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,010 control chromosomes in the GnomAD database, including 39,833 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 39833 hom., cov: 31)

Consequence

ZNF445
NM_181489.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318
Variant links:
Genes affected
ZNF445 (HGNC:21018): (zinc finger protein 445) Enables double-stranded methylated DNA binding activity. Involved in maintenance of DNA methylation and regulation of genetic imprinting. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZNF445NM_181489.6 linkuse as main transcriptc.429+1172A>T intron_variant ENST00000396077.8 NP_852466.1 P59923
ZNF445NM_001369454.1 linkuse as main transcriptc.429+1172A>T intron_variant NP_001356383.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF445ENST00000396077.8 linkuse as main transcriptc.429+1172A>T intron_variant 1 NM_181489.6 ENSP00000379387.2 P59923
ZNF445ENST00000425708.6 linkuse as main transcriptc.429+1172A>T intron_variant 1 ENSP00000413073.2 P59923
ZNF445ENST00000460529.1 linkuse as main transcriptn.597+1172A>T intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.719
AC:
109150
AN:
151892
Hom.:
39789
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.723
Gnomad AMI
AF:
0.589
Gnomad AMR
AF:
0.802
Gnomad ASJ
AF:
0.757
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.919
Gnomad FIN
AF:
0.621
Gnomad MID
AF:
0.763
Gnomad NFE
AF:
0.676
Gnomad OTH
AF:
0.729
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.719
AC:
109252
AN:
152010
Hom.:
39833
Cov.:
31
AF XY:
0.723
AC XY:
53683
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.723
Gnomad4 AMR
AF:
0.802
Gnomad4 ASJ
AF:
0.757
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.920
Gnomad4 FIN
AF:
0.621
Gnomad4 NFE
AF:
0.676
Gnomad4 OTH
AF:
0.732
Alfa
AF:
0.692
Hom.:
4497
Bravo
AF:
0.731
Asia WGS
AF:
0.946
AC:
3291
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.0
DANN
Benign
0.66

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: rs1106499; hg19: chr3-44495441; API