NM_152520.6:c.298+25387T>A

Variant names:

• chr2-179744116-A-T
• rs17824619
• NM_152520.6:c.298+25387T>A

Variant summary

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

The NM_152520.6(ZNF385B):​c.298+25387T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,146 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152520.6. 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
	ZNF385B	NM_152520.6	MANE Select	c.298+25387T>A		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.436+1597T>A		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+25387T>A		intron	N/A	NP_001339739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.298+25387T>A		intron	N/A	ENSP00000386845.2
	ZNF385B	ENST00000409343.5	TSL:2	c.25+1597T>A		intron	N/A	ENSP00000386379.1
	ZNF385B	ENST00000475539.5	TSL:4	n.142+1597T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15838 AN: 152030 Hom.: 1094 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.104 AC: 15840 AN: 152146 Hom.: 1099 Cov.: 32 AF XY: 0.104 AC XY: 7706 AN XY: 74360

African (AFR) AF: 0.0275 AC: 1142 AN: 41538

American (AMR) AF: 0.183 AC: 2793 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5176

South Asian (SAS) AF: 0.145 AC: 701 AN: 4818

European-Finnish (FIN) AF: 0.0830 AC: 879 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9294 AN: 67982

Other (OTH) AF: 0.116 AC: 246 AN: 2116

Alfa AF: 0.118 Hom.: 171

Bravo AF: 0.109

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		1.8
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: rs17824619; hg19: chr2-180608843;