rs13093220

chr3-75721604-A-T

Variant summary

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

The ENST00000668145.1(LINC00960):n.471-18989A>T variant causes a intron, non coding transcript 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: LINC00960 ENST00000668145.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZNF717	XM_047447041.1	c.380-5063T>A		intron_variant
ZNF717	XR_007090409.1	n.412-5063T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00960	ENST00000668145.1	n.471-18989A>T		intron_variant, non_coding_transcript_variant
ZNF717	ENST00000491507.1	n.545-5063T>A		intron_variant, non_coding_transcript_variant		2
ZNF717	ENST00000648506.1	n.833-5063T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.418

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13093220; hg19: chr3-75770755;