rs1035458

Positions:

• chr19-12405336-C-T

Variant summary

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

The XM_047439649.1(ZNF799):​c.3+8623G>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: ZNF799 XM_047439649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

ZNF799 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF799	XM_047439649.1	c.3+8623G>A		intron_variant			XP_047295605.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.685

Alfa AF: 0.691 Hom.: 47676

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

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: rs1035458; hg19: chr19-12516150;