Variant rs7197717 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024706.5(ZNF668):c.-23+1905T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,996 control chromosomes in the GnomAD database, including 16,769 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 0.45 ( 16769 hom., cov: 33)

Consequence

ZNF668
NM_024706.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.639

Variant links:

Genes affected

ZNF668 (HGNC:25821): (zinc finger protein 668) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF668 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF668	NM_024706.5 linkuse as main transcript	c.-23+1905T>G		intron_variant		ENST00000300849.5	NP_078982.3
ZNF668	NM_001172668.2 linkuse as main transcript	c.-23+986T>G		intron_variant			NP_001166139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF668	ENST00000300849.5 linkuse as main transcript	c.-23+1905T>G		intron_variant		1	NM_024706.5	ENSP00000300849	P1

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68630

AN:

151878

Hom.:

16731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.715

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.388

Gnomad OTH

AF:

0.404

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

GnomAD4 genome

AF:

0.452

AC:

68721

AN:

151996

Hom.:

16769

Cov.:

AF XY:

0.454

AC XY:

33702

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.617

Gnomad4 AMR

AF:

0.423

Gnomad4 ASJ

AF:

0.297

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.714

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.388

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.345

Hom.:

2878

Bravo

AF:

0.451

Asia WGS

AF:

0.469

AC:

1628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over