rs475188

Variant names:

• chr19-52646714-C-A
• rs475188
• NM_001277945.2:c.-449+8847G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-52646714-C-A
• chr19-52646714-C-G
• chr19-52646714-C-T

Variant summary

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

The NM_001277945.2(ZNF83):​c.-449+8847G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,966 control chromosomes in the GnomAD database, including 20,445 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 0.51 (20445 hom., cov: 31)
• Consequence: ZNF83 NM_001277945.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 7 publications found

Genes affected

ZNF83 (HGNC:13158): (zinc finger protein 83) 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000269825 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277945.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF83	NM_001277945.2		c.-449+8847G>T		intron	N/A	NP_001264874.1	P51522-1
	ZNF83	NM_001277946.2		c.-234+8847G>T		intron	N/A	NP_001264875.1	P51522-1
	ZNF83	NM_001277947.2		c.-322+8847G>T		intron	N/A	NP_001264876.1	P51522-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269825	ENST00000687234.1		c.142+8847G>T		intron	N/A	ENSP00000509087.2	A0A8I5KXN5
	ENSG00000269825	ENST00000594682.6	TSL:4	n.142+8847G>T		intron	N/A	ENSP00000472147.2	M0R287
	ENSG00000269825	ENST00000595171.5	TSL:4	n.142+8847G>T		intron	N/A	ENSP00000516276.1	M0R287

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77325 AN: 151848 Hom.: 20395 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.510 AC: 77428 AN: 151966 Hom.: 20445 Cov.: 31 AF XY: 0.510 AC XY: 37862 AN XY: 74272

African (AFR) AF: 0.611 AC: 25286 AN: 41412

American (AMR) AF: 0.604 AC: 9220 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3666 AN: 5178

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4828

European-Finnish (FIN) AF: 0.445 AC: 4688 AN: 10546

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29348 AN: 67948

Other (OTH) AF: 0.487 AC: 1029 AN: 2112

Alfa AF: 0.430 Hom.: 8702

Bravo AF: 0.526

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.39
PhyloP100		-3.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs475188; hg19: chr19-53149967;