rs1012531

Positions:

• chr19-52615025-A-C
• chr19-52615025-A-G
• chr19-52615025-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277948.2(ZNF83):​c.-233-228T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,104 control chromosomes in the GnomAD database, including 3,764 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 0.20 (3764 hom., cov: 32)
• Consequence: ZNF83 NM_001277948.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.990

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF83	NM_018300.4	c.-233-228T>G		intron_variant		ENST00000301096.8	NP_060770.3
ZNF83	NM_001277948.2	c.-233-228T>G		intron_variant			NP_001264877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF83	ENST00000301096.8	c.-233-228T>G		intron_variant		3	NM_018300.4	ENSP00000301096	P1
	ENST00000702778.1	n.82-6074A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30889 AN: 151986 Hom.: 3755 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.203 AC: 30918 AN: 152104 Hom.: 3764 Cov.: 32 AF XY: 0.209 AC XY: 15545 AN XY: 74358

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.189

Alfa AF: 0.183 Hom.: 4339

Bravo AF: 0.218

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs1012531; hg19: chr19-53118278;