rs9640842

chr7-127431409-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF800	ENST00000439506.1	c.-59+460G>A		intron_variant		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

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.318

Alfa AF: 0.367 Hom.: 6345

Bravo AF: 0.308

Asia WGS AF: 0.568 AC: 1972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.0
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9640842; hg19: chr7-127071463;