rs1051500

Positions:

• chr19-58433035-A-G

Variant summary

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

The ENST00000254166.4(ZNF132):​c.*288T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 441,290 control chromosomes in the GnomAD database, including 57,915 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 0.55 (24281 hom., cov: 31)
  • Exomes 𝑓: 0.47 (33634 hom.)
• Consequence: ZNF132 ENST00000254166.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

ZNF132 (HGNC:12916): (zinc finger protein 132) 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]

ZNF324B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF132	NM_003433.4	c.*288T>C		3_prime_UTR_variant	3/3	ENST00000254166.4	NP_003424.3
ZNF132	XM_047439361.1	c.*288T>C		3_prime_UTR_variant	3/3		XP_047295317.1
ZNF324B	XM_047438807.1	c.-5-6406A>G		intron_variant			XP_047294763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF132	ENST00000254166.4	c.*288T>C		3_prime_UTR_variant	3/3	1	NM_003433.4	ENSP00000254166	P1
ZNF132	ENST00000703732.1	n.2875T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82962 AN: 151764 Hom.: 24242 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.471 AC: 136320 AN: 289408 Hom.: 33634 Cov.: 2 AF XY: 0.467 AC XY: 70453 AN XY: 151010

Gnomad4 AFR exome AF: 0.766

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.423

Gnomad4 EAS exome AF: 0.285

Gnomad4 SAS exome AF: 0.401

Gnomad4 FIN exome AF: 0.532

Gnomad4 NFE exome AF: 0.489

Gnomad4 OTH exome AF: 0.482

GnomAD4 genome AF: 0.547 AC: 83054 AN: 151882 Hom.: 24281 Cov.: 31 AF XY: 0.537 AC XY: 39861 AN XY: 74218

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.480

Alfa AF: 0.483 Hom.: 28748

Bravo AF: 0.548

Asia WGS AF: 0.417 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1051500; hg19: chr19-58944402;