rs393195

chr19-43988990-T-G

Variant summary

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

The NM_198089.3(ZNF155):c.15+432T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 153,742 control chromosomes in the GnomAD database, including 10,998 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 0.37 (10897 hom., cov: 32)
  • Exomes 𝑓: 0.33 (101 hom.)
• Consequence: ZNF155 NM_198089.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

ZNF155 (HGNC:12940): (zinc finger protein 155) Predicted to enable DNA-binding transcription factor 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF155	NM_198089.3	c.15+432T>G		intron_variant		ENST00000270014.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF155	ENST00000270014.7	c.15+432T>G		intron_variant		1	NM_198089.3	P2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55507 AN: 151926 Hom.: 10873 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.364

GnomAD4 exome AF: 0.325 AC: 552 AN: 1698 Hom.: 101 Cov.: 0 AF XY: 0.320 AC XY: 275 AN XY: 860

Gnomad4 AFR exome AF: 0.563

Gnomad4 AMR exome AF: 0.450

Gnomad4 ASJ exome AF: 0.355

Gnomad4 EAS exome AF: 0.477

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.328

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.364

GnomAD4 genome AF: 0.365 AC: 55571 AN: 152044 Hom.: 10897 Cov.: 32 AF XY: 0.370 AC XY: 27473 AN XY: 74326

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.368

Alfa AF: 0.307 Hom.: 3459

Bravo AF: 0.387

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	3.7
Dann	Benign	0.87

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: rs393195; hg19: chr19-44493142;