2-179715548-T-C

Variant names:

• chr2-179715548-T-C
• rs881737
• NM_152520.6:c.298+53955A>G

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+53955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,950 control chromosomes in the GnomAD database, including 7,441 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 (7441 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	NM_152520.6	MANE Select	c.298+53955A>G		intron	N/A	NP_689733.4
	ZNF385B	NM_001352809.2		c.436+30165A>G		intron	N/A	NP_001339738.1
	ZNF385B	NM_001352810.2		c.298+53955A>G		intron	N/A	NP_001339739.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385B	ENST00000410066.7	TSL:1 MANE Select	c.298+53955A>G		intron	N/A	ENSP00000386845.2	A0A2U3TZT0
	ZNF385B	ENST00000409343.5	TSL:2	c.25+30165A>G		intron	N/A	ENSP00000386379.1	Q569K4-2
	ZNF385B	ENST00000475539.5	TSL:4	n.142+30165A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46503 AN: 151832 Hom.: 7415 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.306 AC: 46553 AN: 151950 Hom.: 7441 Cov.: 32 AF XY: 0.310 AC XY: 23005 AN XY: 74276

African (AFR) AF: 0.316 AC: 13118 AN: 41454

American (AMR) AF: 0.216 AC: 3299 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2577 AN: 5156

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3841 AN: 10534

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20176 AN: 67942

Other (OTH) AF: 0.294 AC: 621 AN: 2112

Alfa AF: 0.285 Hom.: 995

Bravo AF: 0.295

Asia WGS AF: 0.411 AC: 1426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.36
PhyloP100		-0.40
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: rs881737; hg19: chr2-180580275;