19-12405336-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595562.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268870	ENST00000595562.1	TSL:4	c.4-11913G>A		intron	N/A	ENSP00000471613.1	M0R135

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1035458;

hg19: chr19-12516150;