rs1963442

chr3-75740820-G-Achr3-75740820-G-C

Variant summary

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

The NM_001290208.3(ZNF717):c.277+456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 140,264 control chromosomes in the GnomAD database, including 36,594 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 0.75 (36594 hom., cov: 31)
• Consequence: ZNF717 NM_001290208.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF717	NM_001290208.3	c.277+456C>T		intron_variant		ENST00000652011.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF717	ENST00000652011.2	c.277+456C>T		intron_variant			NM_001290208.3	P1
LINC00960	ENST00000668145.1	n.698G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.746 AC: 104523 AN: 140164 Hom.: 36557 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.746 AC: 104605 AN: 140264 Hom.: 36594 Cov.: 31 AF XY: 0.748 AC XY: 51319 AN XY: 68576

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1963442; hg19: chr3-75789971;