rs10938799

chr4-10441801-G-Achr4-10441801-G-T

Variant summary

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

The NM_053042.3(ZNF518B):c.*1303C>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 0.216 in 152,252 control chromosomes in the GnomAD database, including 3,897 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 0.22 (3896 hom., cov: 33)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: ZNF518B NM_053042.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

ZNF518B (HGNC:29365): (zinc finger protein 518B) 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF518B	NM_053042.3	c.*1303C>T		3_prime_UTR_variant	3/3	ENST00000326756.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF518B	ENST00000326756.4	c.*1303C>T		3_prime_UTR_variant	3/3	3	NM_053042.3	P1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32859 AN: 152092 Hom.: 3899 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.310 AC: 13 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.281 AC XY: 9 AN XY: 32

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.289

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.216 AC: 32861 AN: 152210 Hom.: 3896 Cov.: 33 AF XY: 0.219 AC XY: 16320 AN XY: 74416

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.210

Alfa AF: 0.244 Hom.: 2526

Bravo AF: 0.210

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.4
Dann	Benign	0.30

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: rs10938799; hg19: chr4-10443425;