19-58433035-A-G

Variant names:

• chr19-58433035-A-G
• rs1051500
• NM_003433.4:c.*288T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003433.4(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 NM_003433.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 18 publications found

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: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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF132	NM_003433.4	c.*288T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000254166.4	NP_003424.3
ZNF132	XM_047439361.1	c.*288T>C		3_prime_UTR_variant	Exon 3 of 3		XP_047295317.1
ZNF324B	XM_047438807.1	c.-5-6406A>G		intron_variant	Intron 1 of 4		XP_047294763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF132	ENST00000254166.4	c.*288T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_003433.4	ENSP00000254166.2
ZNF132	ENST00000703732.1	n.2875T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ZNF132	ENST00000599148.1	n.*194T>C		downstream_gene_variant		6

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

African (AFR) AF: 0.766 AC: 7194 AN: 9386

American (AMR) AF: 0.360 AC: 3704 AN: 10300

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 4010 AN: 9476

East Asian (EAS) AF: 0.285 AC: 5949 AN: 20858

South Asian (SAS) AF: 0.401 AC: 9524 AN: 23732

European-Finnish (FIN) AF: 0.532 AC: 9033 AN: 16994

Middle Eastern (MID) AF: 0.404 AC: 548 AN: 1356

European-Non Finnish (NFE) AF: 0.489 AC: 88093 AN: 180144

Other (OTH) AF: 0.482 AC: 8265 AN: 17162

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

African (AFR) AF: 0.767 AC: 31790 AN: 41446

American (AMR) AF: 0.399 AC: 6101 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5160

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4820

European-Finnish (FIN) AF: 0.508 AC: 5345 AN: 10516

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33178 AN: 67896

Other (OTH) AF: 0.480 AC: 1010 AN: 2102

Alfa AF: 0.502 Hom.: 55416

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
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1051500; hg19: chr19-58944402;