rs9288039

Variant names:

• chr2-179512573-G-A
• rs9288039
• NM_152520.6:c.552+5955C>T

Variant summary

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

The NM_152520.6(ZNF385B):​c.552+5955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,074 control chromosomes in the GnomAD database, including 40,389 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 0.72 (40389 hom., cov: 32)
• Consequence: ZNF385B NM_152520.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385B	NM_152520.6	c.552+5955C>T		intron_variant	Intron 5 of 9	ENST00000410066.7	NP_689733.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385B	ENST00000410066.7	c.552+5955C>T		intron_variant	Intron 5 of 9	1	NM_152520.6	ENSP00000386845.2

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109552 AN: 151956 Hom.: 40365 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.721 AC: 109612 AN: 152074 Hom.: 40389 Cov.: 32 AF XY: 0.726 AC XY: 53944 AN XY: 74334

African (AFR) AF: 0.563 AC: 23345 AN: 41432

American (AMR) AF: 0.785 AC: 11978 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3468

East Asian (EAS) AF: 0.911 AC: 4726 AN: 5190

South Asian (SAS) AF: 0.751 AC: 3613 AN: 4814

European-Finnish (FIN) AF: 0.805 AC: 8520 AN: 10586

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52657 AN: 67996

Other (OTH) AF: 0.693 AC: 1465 AN: 2114

Alfa AF: 0.752 Hom.: 32022

Bravo AF: 0.713

Asia WGS AF: 0.809 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.62
PhyloP100		-0.52
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: rs9288039; hg19: chr2-180377300;