rs13239338

chr7-127344319-C-Achr7-127344319-C-T

Variant summary

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

The XM_006715867.5(ZNF800):c.*3538G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,956 control chromosomes in the GnomAD database, including 1,068 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 0.10 (1068 hom., cov: 33)
• Consequence: ZNF800 XM_006715867.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

Genes affected

ZNF800 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF800	XM_006715867.5	c.*3538G>T		3_prime_UTR_variant	6/6
ZNF800	XM_006715868.5	c.*3538G>T		3_prime_UTR_variant	6/6
ZNF800	XM_006715869.5	c.*3538G>T		3_prime_UTR_variant	5/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15870 AN: 151838 Hom.: 1068 Cov.: 33

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.104 AC: 15858 AN: 151956 Hom.: 1068 Cov.: 33 AF XY: 0.105 AC XY: 7786 AN XY: 74256

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0395 Hom.: 36

Bravo AF: 0.0975

Asia WGS AF: 0.0770 AC: 268 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.28
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13239338; hg19: chr7-126984373;