rs393195

Variant names:

• chr19-43988990-T-G
• rs393195
• NM_198089.3:c.15+432T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001260488.2(ZNF155):​c.-42+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_001260488.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001260488.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF155	NM_198089.3	MANE Select	c.15+432T>G		intron	N/A	NP_932355.3
	ZNF155	NM_001260488.2		c.-42+432T>G		intron	N/A	NP_001247417.2
	ZNF155	NM_001260486.2		c.15+432T>G		intron	N/A	NP_001247415.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF155	ENST00000270014.7	TSL:1 MANE Select	c.15+432T>G		intron	N/A	ENSP00000270014.1
	ZNF155	ENST00000590615.5	TSL:1	c.15+432T>G		intron	N/A	ENSP00000465691.1
	ZNF155	ENST00000407951.6	TSL:2	c.-42+432T>G		intron	N/A	ENSP00000385163.2

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

African (AFR) AF: 0.563 AC: 45 AN: 80

American (AMR) AF: 0.450 AC: 36 AN: 80

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 27 AN: 76

East Asian (EAS) AF: 0.477 AC: 42 AN: 88

South Asian (SAS) AF: 0.150 AC: 6 AN: 40

European-Finnish (FIN) AF: 0.328 AC: 19 AN: 58

Middle Eastern (MID) AF: 0.500 AC: 6 AN: 12

European-Non Finnish (NFE) AF: 0.287 AC: 331 AN: 1154

Other (OTH) AF: 0.364 AC: 40 AN: 110

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

African (AFR) AF: 0.481 AC: 19958 AN: 41454

American (AMR) AF: 0.442 AC: 6747 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2859 AN: 5172

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4826

European-Finnish (FIN) AF: 0.286 AC: 3019 AN: 10554

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18969 AN: 67980

Other (OTH) AF: 0.368 AC: 777 AN: 2114

Alfa AF: 0.308 Hom.: 3890

Bravo AF: 0.387

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.7
DANN	Benign	0.87
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs393195; hg19: chr19-44493142;