rs7197717

Positions:

• chr16-31071754-A-C
• chr16-31071754-A-G
• chr16-31071754-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

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]

ACMG classification

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	UniProt
ZNF668	NM_024706.5	c.-23+1905T>G		intron_variant		ENST00000300849.5
ZNF668	NM_001172668.2	c.-23+986T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68630 AN: 151878 Hom.: 16731 Cov.: 33

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.: 33 AF XY: 0.454 AC XY: 33702 AN XY: 74272

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

Other links and lift over

dbSNP: rs7197717; hg19: chr16-31083075;