7-100067194-A-G

Position:

• chr7-100067194-A-G

Variant summary

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

The ENST00000413658.6(ZNF3):​c.272-2282T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,084 control chromosomes in the GnomAD database, including 3,492 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 0.21 (3492 hom., cov: 32)
• Consequence: ZNF3 ENST00000413658.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

ZNF3 (HGNC:13089): (zinc finger protein 3) Enables identical protein binding activity. Predicted to be involved in negative 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF3	NM_001318137.2	c.164-2282T>C		intron_variant
ZNF3	NM_001371210.1	c.272-2282T>C		intron_variant
ZNF3	NM_017715.4	c.272-2282T>C		intron_variant
ZNF3	XM_047420802.1	c.272-2282T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF3	ENST00000413658.6	c.272-2282T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31536 AN: 151966 Hom.: 3492 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.207 AC: 31545 AN: 152084 Hom.: 3492 Cov.: 32 AF XY: 0.204 AC XY: 15164 AN XY: 74356

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.207

Alfa AF: 0.222 Hom.: 5389

Bravo AF: 0.201

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7778571; hg19: chr7-99664817;