rs2271759

chr2-179483518-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_152520.6(ZNF385B):c.553-84A>C variant causes a intron change. The variant allele was found at a frequency of 0.291 in 1,556,866 control chromosomes in the GnomAD database, including 67,223 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 0.31 (7558 hom., cov: 32)
  • Exomes 𝑓: 0.29 (59665 hom.)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.70

Genes affected

ZNF385B (HGNC:26332): (zinc finger protein 385B) Enables p53 binding activity. Involved in intrinsic apoptotic signaling pathway by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385B	NM_152520.6	c.553-84A>C		intron_variant		ENST00000410066.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385B	ENST00000410066.7	c.553-84A>C		intron_variant		1	NM_152520.6	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47095 AN: 151896 Hom.: 7546 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.289 AC: 405866 AN: 1404852 Hom.: 59665 AF XY: 0.289 AC XY: 201422 AN XY: 697960

Gnomad4 AFR exome AF: 0.368

Gnomad4 AMR exome AF: 0.298

Gnomad4 ASJ exome AF: 0.264

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.279

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.282

Gnomad4 OTH exome AF: 0.297

GnomAD4 genome AF: 0.310 AC: 47156 AN: 152014 Hom.: 7558 Cov.: 32 AF XY: 0.311 AC XY: 23070 AN XY: 74298

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.297

Alfa AF: 0.290 Hom.: 3997

Bravo AF: 0.313

Asia WGS AF: 0.421 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	15
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: rs2271759; hg19: chr2-180348245; COSMIC: COSV61177889;