rs3009034

Variant names:

• chr3-75732427-T-C
• rs3009034
• NM_001324027.1:c.2167-306A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001324027.1(ZNF717):​c.2167-306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.60 (19987 hom., cov: 35)
  • Failed GnomAD Quality Control
• Consequence: ZNF717 NM_001324027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324027.1. 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
	ZNF717	NM_001324027.1		c.2167-306A>G		intron	N/A	NP_001310956.1
	ZNF717	NM_001290210.2		c.278-306A>G		intron	N/A	NP_001277139.1	C9J5W8
	ZNF717	NM_001324026.2		c.278-306A>G		intron	N/A	NP_001310955.1	C9J5W8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF717	ENST00000477374.5	TSL:2	c.278-306A>G		intron	N/A	ENSP00000417902.1	C9J5W8
	ZNF717	ENST00000491507.1	TSL:2	n.544+8849A>G		intron	N/A
	ZNF717	ENST00000648506.1		n.832+8849A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 88307 AN: 147016 Hom.: 19955 Cov.: 35

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.607

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.601 AC: 88375 AN: 147118 Hom.: 19987 Cov.: 35 AF XY: 0.607 AC XY: 43590 AN XY: 71784

African (AFR) AF: 0.581 AC: 23440 AN: 40338

American (AMR) AF: 0.597 AC: 8760 AN: 14678

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1891 AN: 3372

East Asian (EAS) AF: 0.706 AC: 3529 AN: 5002

South Asian (SAS) AF: 0.649 AC: 3026 AN: 4662

European-Finnish (FIN) AF: 0.667 AC: 6798 AN: 10186

Middle Eastern (MID) AF: 0.613 AC: 174 AN: 284

European-Non Finnish (NFE) AF: 0.593 AC: 38970 AN: 65672

Other (OTH) AF: 0.607 AC: 1238 AN: 2040

Alfa AF: 0.712 Hom.: 6788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.15
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3009034;

hg19: chr3-75781578;