9-111530912-G-A

Variant names:

• chr9-111530912-G-A
• rs200679867
• NM_133464.5:c.450G>A

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_133464.5(ZNF483):​c.450G>A​(p.Glu150Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000969 in 1,548,304 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000073 (0 hom., cov: 26)
  • Exomes 𝑓: 0.000099 (0 hom.)
• Consequence: ZNF483 NM_133464.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.751
• Publications: 0 publications found

Genes affected

ZNF483 (HGNC:23384): (zinc finger protein 483) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 9-111530912-G-A is Benign according to our data. Variant chr9-111530912-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3987490.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.751 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF483	NM_133464.5	c.450G>A	p.Glu150Glu	synonymous_variant	Exon 3 of 6	ENST00000309235.6	NP_597721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF483	ENST00000309235.6	c.450G>A	p.Glu150Glu	synonymous_variant	Exon 3 of 6	1	NM_133464.5	ENSP00000311679.5
ZNF483	ENST00000355824.7	c.450G>A	p.Glu150Glu	synonymous_variant	Exon 3 of 6	1		ENSP00000438048.1
ZNF483	ENST00000358151.8	c.450G>A	p.Glu150Glu	synonymous_variant	Exon 3 of 6	2		ENSP00000350871.4

Frequencies

GnomAD3 genomes AF: 0.0000732 AC: 11 AN: 150212 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000199

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: 0.0000889

Gnomad OTH AF: 0.000972

GnomAD2 exomes AF: 0.0000695 AC: 17 AN: 244718 AF XY: 0.0000680

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000244

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000463

Gnomad NFE exome AF: 0.0000718

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000994 AC: 139 AN: 1397982 Hom.: 0 Cov.: 28 AF XY: 0.000105 AC XY: 73 AN XY: 695934

African (AFR) AF: 0.00 AC: 0 AN: 32376

American (AMR) AF: 0.000233 AC: 10 AN: 42960

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23928

East Asian (EAS) AF: 0.00 AC: 0 AN: 37698

South Asian (SAS) AF: 0.00 AC: 0 AN: 80484

European-Finnish (FIN) AF: 0.0000206 AC: 1 AN: 48442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5492

European-Non Finnish (NFE) AF: 0.000116 AC: 124 AN: 1070112

Other (OTH) AF: 0.0000708 AC: 4 AN: 56490

GnomAD4 genome AF: 0.0000732 AC: 11 AN: 150322 Hom.: 0 Cov.: 26 AF XY: 0.0000818 AC XY: 6 AN XY: 73386

African (AFR) AF: 0.00 AC: 0 AN: 41046

American (AMR) AF: 0.000199 AC: 3 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3446

East Asian (EAS) AF: 0.00 AC: 0 AN: 5118

South Asian (SAS) AF: 0.00 AC: 0 AN: 4720

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10196

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.0000889 AC: 6 AN: 67458

Other (OTH) AF: 0.000962 AC: 2 AN: 2080

Alfa AF: 0.0000987 Hom.: 0

Bravo AF: 0.0000680

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Jun 07, 2025

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.54
PhyloP100		0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs200679867; hg19: chr9-114293192;