ENST00000439506.1:c.-59+460G>A

Variant names:

• chr7-127431409-C-T
• rs9640842
• ENST00000439506.1:c.-59+460G>A

Variant summary

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

The ENST00000439506.1(ZNF800):​c.-59+460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,996 control chromosomes in the GnomAD database, including 10,133 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 0.32 (10133 hom., cov: 32)
• Consequence: ZNF800 ENST00000439506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 4 publications found

Genes affected

ZNF800 (HGNC:27267): (zinc finger protein 800) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439506.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF800	ENST00000439506.1	TSL:1	c.-59+460G>A		intron	N/A	ENSP00000389776.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48738 AN: 151878 Hom.: 10121 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.321 AC: 48757 AN: 151996 Hom.: 10133 Cov.: 32 AF XY: 0.331 AC XY: 24589 AN XY: 74264

African (AFR) AF: 0.0800 AC: 3319 AN: 41474

American (AMR) AF: 0.389 AC: 5946 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3466

East Asian (EAS) AF: 0.801 AC: 4149 AN: 5182

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4816

European-Finnish (FIN) AF: 0.448 AC: 4720 AN: 10528

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26363 AN: 67948

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.372 Hom.: 9191

Bravo AF: 0.308

Asia WGS AF: 0.568 AC: 1972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.25
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs9640842; hg19: chr7-127071463;