rs17638629

chr19-12114557-T-G

Variant summary

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

The NR_171040.1(ZNF788P):n.3734T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 152,330 control chromosomes in the GnomAD database, including 226 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 0.036 (226 hom., cov: 32)
  • Exomes 𝑓: 0.045 (0 hom.)
• Consequence: ZNF788P NR_171040.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

ZNF788P (HGNC:):

ZNF20 (HGNC:12992): (zinc finger protein 20) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF788P	NR_171040.1	n.3734T>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000601686.1	n.165-21218T>G		intron_variant, non_coding_transcript_variant		4
ZNF20	ENST00000600335.5	c.191+20943A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0363 AC: 5519 AN: 152190 Hom.: 218 Cov.: 32

Gnomad AFR AF: 0.00827

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0315

GnomAD4 exome AF: 0.0455 AC: 1 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 1 AN XY: 14

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.0500

GnomAD4 genome AF: 0.0364 AC: 5539 AN: 152308 Hom.: 226 Cov.: 32 AF XY: 0.0371 AC XY: 2762 AN XY: 74480

Gnomad4 AFR AF: 0.00825

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0396

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0364 Hom.: 239

Bravo AF: 0.0419

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17638629; hg19: chr19-12225372;