16-75170384-C-A

Position:

• chr16-75170384-C-A

Variant summary

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

The NM_153688.4(ZFP1):​c.*50C>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 0.127 in 1,507,764 control chromosomes in the GnomAD database, including 20,063 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 0.11 (1932 hom., cov: 32)
  • Exomes 𝑓: 0.13 (18131 hom.)
• Consequence: ZFP1 NM_153688.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

ZFP1 (HGNC:23328): (ZFP1 zinc finger protein) This gene belongs to the zinc finger protein family. Some members of this family bind to DNA by zinc-mediated secondary structures called zinc fingers, and are involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFP1	NM_153688.4	c.*50C>A		3_prime_UTR_variant	4/4	ENST00000570010.6	NP_710155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFP1	ENST00000570010.6	c.*50C>A		3_prime_UTR_variant	4/4	2	NM_153688.4	ENSP00000457044	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17327 AN: 151986 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.108

GnomAD3 exomes AF: 0.176 AC: 30606 AN: 174116 Hom.: 4685 AF XY: 0.175 AC XY: 16157 AN XY: 92418

Gnomad AFR exome AF: 0.0425

Gnomad AMR exome AF: 0.189

Gnomad ASJ exome AF: 0.0911

Gnomad EAS exome AF: 0.622

Gnomad SAS exome AF: 0.283

Gnomad FIN exome AF: 0.142

Gnomad NFE exome AF: 0.105

Gnomad OTH exome AF: 0.155

GnomAD4 exome AF: 0.129 AC: 174443 AN: 1355662 Hom.: 18131 Cov.: 31 AF XY: 0.132 AC XY: 87373 AN XY: 663196

Gnomad4 AFR exome AF: 0.0419

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.0890

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.114 AC: 17326 AN: 152102 Hom.: 1932 Cov.: 32 AF XY: 0.120 AC XY: 8952 AN XY: 74326

Gnomad4 AFR AF: 0.0435

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0946 Hom.: 534

Bravo AF: 0.113

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.10
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764551; hg19: chr16-75204282; COSMIC: COSV60032794; COSMIC: COSV60032794;