rs4801163

chr19-56464017-G-T

Variant summary

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

The NM_001321356.2(ZNF667):c.-59-1588C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,002 control chromosomes in the GnomAD database, including 11,844 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 0.39 (11844 hom., cov: 32)
• Consequence: ZNF667 NM_001321356.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596

Genes affected

ZNF667 (HGNC:28854): (zinc finger protein 667) Predicted to enable DNA-binding transcription factor activity 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 located 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF667	NM_001321356.2	c.-59-1588C>A		intron_variant		ENST00000504904.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF667	ENST00000504904.8	c.-59-1588C>A		intron_variant		2	NM_001321356.2	P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59118 AN: 151884 Hom.: 11840 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.389 AC: 59150 AN: 152002 Hom.: 11844 Cov.: 32 AF XY: 0.385 AC XY: 28596 AN XY: 74310

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.407

Alfa AF: 0.425 Hom.: 6570

Bravo AF: 0.388

Asia WGS AF: 0.251 AC: 878 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.89
Dann	Benign	0.78

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: rs4801163; hg19: chr19-56975386;