rs1478462

Variant names:

• chr19-37656124-A-G
• rs1478462
• ENST00000514101.6:c.-250T>C

Variant summary

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

The NM_001320668.3(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 NM_001320668.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320668.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP30	NM_001320668.3		c.-250T>C		5_prime_UTR	Exon 1 of 6	NP_001307597.1	Q9Y2G7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP30	ENST00000514101.6	TSL:1	c.-250T>C		5_prime_UTR	Exon 1 of 6	ENSP00000422930.2	Q9Y2G7
	ZFP30	ENST00000937928.1		c.-156T>C		5_prime_UTR	Exon 1 of 6	ENSP00000607987.1
	ZFP30	ENST00000937929.1		c.-250T>C		5_prime_UTR	Exon 1 of 6	ENSP00000607988.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 2 AN: 6

East Asian (EAS) AF: 0.167 AC: 2 AN: 12

South Asian (SAS) AF: 0.214 AC: 3 AN: 14

European-Finnish (FIN) AF: 0.192 AC: 10 AN: 52

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.234 AC: 128 AN: 546

Other (OTH) AF: 0.346 AC: 9 AN: 26

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

African (AFR) AF: 0.109 AC: 4527 AN: 41510

American (AMR) AF: 0.165 AC: 2516 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3470

East Asian (EAS) AF: 0.122 AC: 631 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1323 AN: 4822

European-Finnish (FIN) AF: 0.221 AC: 2336 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13766 AN: 68008

Other (OTH) AF: 0.197 AC: 416 AN: 2114

Alfa AF: 0.184 Hom.: 337

Bravo AF: 0.167

Asia WGS AF: 0.188 AC: 652 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.48
PhyloP100		0.24
PromoterAI		0.14	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1478462; hg19: chr19-38147025;