chr19-12405336-C-T

Variant names:

• chr19-12405336-C-T
• rs1035458
• ENST00000595562.1:c.4-11913G>A

Variant summary

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

The ENST00000595562.1(ENSG00000268870):​c.4-11913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,046 control chromosomes in the GnomAD database, including 40,462 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 0.71 (40462 hom., cov: 31)
• Consequence: ENSG00000268870 ENST00000595562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 7 publications found

Genes affected

ENSG00000268870 (HGNC:):

ZNF799 (HGNC:28071): (zinc finger protein 799) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ZNF799 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF799	XM_047439649.1	c.3+8623G>A		intron_variant	Intron 1 of 3		XP_047295605.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268870	ENST00000595562.1	c.4-11913G>A		intron_variant	Intron 1 of 3	4		ENSP00000471613.1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108291 AN: 151928 Hom.: 40413 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.713 AC: 108392 AN: 152046 Hom.: 40462 Cov.: 31 AF XY: 0.699 AC XY: 51919 AN XY: 74290

African (AFR) AF: 0.911 AC: 37806 AN: 41506

American (AMR) AF: 0.539 AC: 8223 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2455 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1413 AN: 5174

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4812

European-Finnish (FIN) AF: 0.630 AC: 6627 AN: 10520

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47480 AN: 67982

Other (OTH) AF: 0.685 AC: 1448 AN: 2114

Alfa AF: 0.696 Hom.: 61365

Bravo AF: 0.715

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.27
PhyloP100		-1.8

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: rs1035458; hg19: chr19-12516150;