chr3-75721604-A-T

Variant names:

• chr3-75721604-A-T
• rs13093220
• ENST00000491507.1:n.545-5063T>A

Variant summary

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

The ENST00000491507.1(ZNF717):​n.545-5063T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,122 control chromosomes in the GnomAD database, including 13,653 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 0.42 (13653 hom., cov: 34)
• Consequence: ZNF717 ENST00000491507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

Genes affected

ZNF717 (HGNC:29448): (zinc finger protein 717) This gene encodes a Kruppel-associated box (KRAB) zinc-finger protein, which belongs to a large group of transcriptional regulators in mammals. These proteins bind nucleic acids and play important roles in various cellular functions, including cell proliferation, differentiation and apoptosis, and in regulating viral replication and transcription. A pseudogene of this gene was identified on chromosome 1. [provided by RefSeq, May 2016]

LINC00960 (HGNC:48710): (long intergenic non-protein coding RNA 960)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF717	XM_047447041.1	c.380-5063T>A		intron_variant	Intron 5 of 5		XP_047302997.1
ZNF717	XR_007090409.1	n.412-5063T>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF717	ENST00000491507.1	n.545-5063T>A		intron_variant	Intron 4 of 5	2
ZNF717	ENST00000648506.1	n.833-5063T>A		intron_variant	Intron 4 of 6
LINC00960	ENST00000668145.2	n.517-18989A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63533 AN: 152002 Hom.: 13647 Cov.: 34

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.418 AC: 63589 AN: 152122 Hom.: 13653 Cov.: 34 AF XY: 0.413 AC XY: 30743 AN XY: 74362

African (AFR) AF: 0.355 AC: 14724 AN: 41504

American (AMR) AF: 0.451 AC: 6894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1360 AN: 3464

East Asian (EAS) AF: 0.323 AC: 1669 AN: 5170

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4824

European-Finnish (FIN) AF: 0.483 AC: 5107 AN: 10576

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31286 AN: 67984

Other (OTH) AF: 0.418 AC: 880 AN: 2106

Alfa AF: 0.432 Hom.: 1288

Bravo AF: 0.418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.51
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs13093220; hg19: chr3-75770755;