rs893186

Positions:

• chr19-58457812-C-A

Variant summary

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

The NM_207395.3(ZNF324B):​c.*1233C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,996 control chromosomes in the GnomAD database, including 23,344 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 0.53 (23344 hom., cov: 31)
  • Exomes 𝑓: 0.71 (5 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF324B NM_207395.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

ZNF324B (HGNC:33107): (zinc finger protein 324B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF324B	NM_207395.3	c.*1233C>A		3_prime_UTR_variant	4/4	ENST00000336614.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF324B	ENST00000336614.9	c.*1233C>A		3_prime_UTR_variant	4/4	1	NM_207395.3	P1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80812 AN: 151876 Hom.: 23304 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.465

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.708 AC: 17 AN: 24 Hom.: 5 Cov.: 0 AF XY: 0.700 AC XY: 14 AN XY: 20

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.532 AC: 80901 AN: 151996 Hom.: 23344 Cov.: 31 AF XY: 0.523 AC XY: 38868 AN XY: 74276

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.463

Alfa AF: 0.465 Hom.: 10365

Bravo AF: 0.537

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.41

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: rs893186; hg19: chr19-58969179;