19-52664681-G-T

Position:

• chr19-52664681-G-T

Variant summary

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

The NM_001396016.1(LOC122539214):​c.-19-3838C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 148,578 control chromosomes in the GnomAD database, including 942 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 0.11 (942 hom., cov: 28)
• Consequence: LOC122539214 NM_001396016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

LOC122539214 (HGNC:):

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC122539214	NM_001396016.1	c.-19-3838C>A		intron_variant		ENST00000598322.3
ZNF83	NM_001277948.2	c.-530-3838C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598322.3	c.-19-3838C>A		intron_variant			NM_001396016.1	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 15977 AN: 148448 Hom.: 941 Cov.: 28

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0695

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.000616

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0882

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.108 AC: 15989 AN: 148578 Hom.: 942 Cov.: 28 AF XY: 0.105 AC XY: 7601 AN XY: 72258

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.000617

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0869

Alfa AF: 0.107 Hom.: 304

Bravo AF: 0.107

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12976870; hg19: chr19-53167934;