rs7195303

Variant names:

• chr16-75133681-G-A
• rs7195303
• ENST00000563098.1:n.397+1059G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-75133681-G-A
• chr16-75133681-G-C
• chr16-75133681-G-T

Variant summary

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

The ENST00000563098.1(ENSG00000261058):​n.397+1059G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,308 control chromosomes in the GnomAD database, including 64,486 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 0.92 (64486 hom., cov: 33)
• Consequence: ENSG00000261058 ENST00000563098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 12 publications found

Genes affected

ENSG00000261058 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFP1	XM_011522921.3	c.35+1059G>A		intron_variant	Intron 4 of 6		XP_011521223.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261058	ENST00000563098.1	n.397+1059G>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139886 AN: 152190 Hom.: 64425 Cov.: 33

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.907

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.919 AC: 140004 AN: 152308 Hom.: 64486 Cov.: 33 AF XY: 0.918 AC XY: 68350 AN XY: 74474

African (AFR) AF: 0.942 AC: 39177 AN: 41574

American (AMR) AF: 0.928 AC: 14189 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3245 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3915 AN: 5180

South Asian (SAS) AF: 0.873 AC: 4214 AN: 4826

European-Finnish (FIN) AF: 0.922 AC: 9788 AN: 10618

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62448 AN: 68032

Other (OTH) AF: 0.906 AC: 1916 AN: 2114

Alfa AF: 0.915 Hom.: 130950

Bravo AF: 0.920

Asia WGS AF: 0.831 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.20
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7195303; hg19: chr16-75167579;