chr9-111531354-A-G

Variant names:

• chr9-111531354-A-G
• rs10980926
• NM_133464.5:c.501+391A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133464.5(ZNF483):​c.501+391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 146,762 control chromosomes in the GnomAD database, including 23,172 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 0.56 (23172 hom., cov: 31)
• Consequence: ZNF483 NM_133464.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 28 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF483	NM_133464.5	c.501+391A>G		intron_variant	Intron 3 of 5	ENST00000309235.6	NP_597721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF483	ENST00000309235.6	c.501+391A>G		intron_variant	Intron 3 of 5	1	NM_133464.5	ENSP00000311679.5
ZNF483	ENST00000355824.7	c.501+391A>G		intron_variant	Intron 3 of 5	1		ENSP00000438048.1
ZNF483	ENST00000358151.8	c.501+391A>G		intron_variant	Intron 3 of 5	2		ENSP00000350871.4

Frequencies

GnomAD3 genomes AF: 0.556 AC: 81599 AN: 146634 Hom.: 23158 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.556 AC: 81659 AN: 146762 Hom.: 23172 Cov.: 31 AF XY: 0.549 AC XY: 39458 AN XY: 71858

African (AFR) AF: 0.428 AC: 15610 AN: 36442

American (AMR) AF: 0.460 AC: 6944 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2074 AN: 3462

East Asian (EAS) AF: 0.412 AC: 2131 AN: 5176

South Asian (SAS) AF: 0.514 AC: 2472 AN: 4814

European-Finnish (FIN) AF: 0.625 AC: 6581 AN: 10536

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44124 AN: 67960

Other (OTH) AF: 0.536 AC: 1114 AN: 2080

Alfa AF: 0.595 Hom.: 11585

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10980926; hg19: chr9-114293634; COSMIC: COSV58515007; COSMIC: COSV58515007;