rs1478462

Positions:

• chr19-37656124-A-G

Variant summary

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

The ENST00000514101.6(ZFP30):​c.-250T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,836 control chromosomes in the GnomAD database, including 2,584 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 0.18 (2560 hom., cov: 33)
  • Exomes 𝑓: 0.23 (24 hom.)
• Consequence: ZFP30 ENST00000514101.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

ZFP30 (HGNC:29555): (ZFP30 zinc finger protein) 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP30	NM_001320668.3	c.-250T>C		5_prime_UTR_variant	1/6		NP_001307597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP30	ENST00000514101.6	c.-250T>C		5_prime_UTR_variant	1/6	1		ENSP00000422930	P1
ZFP30	ENST00000587199.5	c.-152+186T>C		intron_variant		4		ENSP00000466993
ZFP30	ENST00000586732.1	n.490-1245T>C		intron_variant, non_coding_transcript_variant		3
ZFP30	ENST00000589676.5	n.283-1245T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26796 AN: 152054 Hom.: 2558 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.195

GnomAD4 exome AF: 0.233 AC: 155 AN: 664 Hom.: 24 Cov.: 0 AF XY: 0.232 AC XY: 115 AN XY: 496

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.214

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.234

Gnomad4 OTH exome AF: 0.346

GnomAD4 genome AF: 0.176 AC: 26819 AN: 152172 Hom.: 2560 Cov.: 33 AF XY: 0.180 AC XY: 13414 AN XY: 74414

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.197

Alfa AF: 0.187 Hom.: 332

Bravo AF: 0.167

Asia WGS AF: 0.188 AC: 652 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478462; hg19: chr19-38147025;