rs13345832

Positions:

• chr19-52637196-C-T

Variant summary

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

The NM_001277948.2(ZNF83):​c.-448-2043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,476 control chromosomes in the GnomAD database, including 320 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 0.063 (318 hom., cov: 31)
  • Exomes 𝑓: 0.072 (2 hom.)
• Consequence: ZNF83 NM_001277948.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF83	NM_018300.4	c.-322+1116G>A		intron_variant		ENST00000301096.8	NP_060770.3
ZNF83	NM_001277948.2	c.-448-2043G>A		intron_variant			NP_001264877.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF83	ENST00000301096.8	c.-322+1116G>A		intron_variant		3	NM_018300.4	ENSP00000301096	P1

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9494 AN: 151998 Hom.: 315 Cov.: 31

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0746

GnomAD4 exome AF: 0.0722 AC: 26 AN: 360 Hom.: 2 AF XY: 0.0714 AC XY: 18 AN XY: 252

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0455

Gnomad4 NFE exome AF: 0.0756

Gnomad4 OTH exome AF: 0.0313

GnomAD4 genome AF: 0.0625 AC: 9509 AN: 152116 Hom.: 318 Cov.: 31 AF XY: 0.0630 AC XY: 4686 AN XY: 74354

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.0548

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0637 Hom.: 324

Bravo AF: 0.0638

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.56

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: rs13345832; hg19: chr19-53140449;