rs3009034

chr3-75732427-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000668145.1(LINC00960):n.471-8166T>C variant causes a intron, non coding transcript 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: LINC00960 ENST00000668145.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd at 19955 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF717	NM_001290210.2	c.278-306A>G		intron_variant
ZNF717	NM_001324026.2	c.278-306A>G		intron_variant
ZNF717	NM_001324027.1	c.2167-306A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00960	ENST00000668145.1	n.471-8166T>C		intron_variant, non_coding_transcript_variant
ZNF717	ENST00000477374.5	c.278-306A>G		intron_variant		2
ZNF717	ENST00000491507.1	n.544+8849A>G		intron_variant, non_coding_transcript_variant		2
ZNF717	ENST00000648506.1	n.832+8849A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.607

Alfa AF: 0.763 Hom.: 3575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.0
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3009034; hg19: chr3-75781578;