rs764551

Variant names:

• chr16-75170384-C-A
• rs764551
• NM_153688.4:c.*50C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-75170384-C-A
• chr16-75170384-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153688.4. 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
	ZFP1	NM_153688.4	MANE Select	c.*50C>A		3_prime_UTR	Exon 4 of 4	NP_710155.2	Q6P2D0-1
	ZFP1	NM_001318469.2		c.*50C>A		3_prime_UTR	Exon 4 of 4	NP_001305398.1	Q6P2D0-1
	ZFP1	NM_001318471.2		c.*50C>A		3_prime_UTR	Exon 5 of 5	NP_001305400.1	J3KNQ1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP1	ENST00000570010.6	TSL:2 MANE Select	c.*50C>A		3_prime_UTR	Exon 4 of 4	ENSP00000457044.1	Q6P2D0-1
	ZFP1	ENST00000393430.6	TSL:1	c.*50C>A		3_prime_UTR	Exon 4 of 4	ENSP00000377080.2	Q6P2D0-1
	ZFP1	ENST00000332307.4	TSL:1	c.*50C>A		3_prime_UTR	Exon 3 of 3	ENSP00000333192.4	J3KNQ1

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

GnomAD2 exomes AF: 0.176 AC: 30606 AN: 174116 AF XY: 0.175

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 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

African (AFR) AF: 0.0419 AC: 1263 AN: 30172

American (AMR) AF: 0.178 AC: 5171 AN: 29084

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 1764 AN: 19816

East Asian (EAS) AF: 0.650 AC: 25206 AN: 38806

South Asian (SAS) AF: 0.272 AC: 18227 AN: 67098

European-Finnish (FIN) AF: 0.139 AC: 6795 AN: 49032

Middle Eastern (MID) AF: 0.106 AC: 529 AN: 5010

European-Non Finnish (NFE) AF: 0.102 AC: 107924 AN: 1060830

Other (OTH) AF: 0.136 AC: 7564 AN: 55814

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

African (AFR) AF: 0.0435 AC: 1806 AN: 41530

American (AMR) AF: 0.137 AC: 2094 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3187 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1380 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10554

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0993 AC: 6755 AN: 67998

Other (OTH) AF: 0.108 AC: 228 AN: 2108

Alfa AF: 0.106 Hom.: 1164

Bravo AF: 0.113

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.10
DANN	Benign	0.53
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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